/**
   * Writes the desired section.
   *
   * @param identification the identification of the project
   * @param identificationFeaturesGenerator the identification features generator of the project
   * @param identificationParameters the identification parameters
   * @param keys the keys of the protein matches to output
   * @param nSurroundingAA the number of surrounding amino acids to export
   * @param linePrefix the line prefix to use.
   * @param validatedOnly whether only validated matches should be exported
   * @param decoys whether decoy matches should be exported as well
   * @param waitingHandler the waiting handler
   * @throws IOException exception thrown whenever an error occurred while interacting with a file
   * @throws SQLException thrown whenever an error occurred while interacting with the database
   * @throws ClassNotFoundException thrown whenever an error occurred while deserializing a match
   *     from the database
   * @throws InterruptedException thrown whenever a threading error occurred while interacting with
   *     the database
   * @throws MzMLUnmarshallerException thrown whenever an error occurred while reading an mzML file
   */
  public void writeSection(
      Identification identification,
      IdentificationFeaturesGenerator identificationFeaturesGenerator,
      IdentificationParameters identificationParameters,
      ArrayList<String> keys,
      int nSurroundingAA,
      String linePrefix,
      boolean validatedOnly,
      boolean decoys,
      WaitingHandler waitingHandler)
      throws IOException, SQLException, ClassNotFoundException, InterruptedException,
          MzMLUnmarshallerException {

    if (waitingHandler != null) {
      waitingHandler.setSecondaryProgressCounterIndeterminate(true);
    }

    if (header) {
      writeHeader();
    }

    if (keys == null) {
      keys = new ArrayList<String>(identification.getPeptideIdentification());
    }

    int line = 1;

    if (waitingHandler != null) {
      waitingHandler.setWaitingText("Exporting. Please Wait...");
      waitingHandler.resetSecondaryProgressCounter();
      waitingHandler.setMaxSecondaryProgressCounter(keys.size());
    }

    PSParameter psParameter = new PSParameter();
    ArrayList<UrParameter> parameters = new ArrayList<UrParameter>(1);
    parameters.add(psParameter);

    PeptideMatchesIterator peptideMatchesIterator =
        identification.getPeptideMatchesIterator(
            keys, parameters, psmSection != null, parameters, waitingHandler);

    while (peptideMatchesIterator.hasNext()) {

      if (waitingHandler != null) {
        if (waitingHandler.isRunCanceled()) {
          return;
        }
        waitingHandler.increaseSecondaryProgressCounter();
      }

      PeptideMatch peptideMatch = peptideMatchesIterator.next();
      String peptideKey = peptideMatch.getKey();
      psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);

      if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {

        if (decoys
            || !peptideMatch
                .getTheoreticPeptide()
                .isDecoy(identificationParameters.getSequenceMatchingPreferences())) {

          boolean first = true;

          if (indexes) {
            if (linePrefix != null) {
              writer.write(linePrefix);
            }
            writer.write(line + "");
            first = false;
          }

          for (ExportFeature exportFeature : peptideFeatures) {
            if (!first) {
              writer.addSeparator();
            } else {
              first = false;
            }
            PsPeptideFeature peptideFeature = (PsPeptideFeature) exportFeature;
            writer.write(
                getfeature(
                    identification,
                    identificationFeaturesGenerator,
                    identificationParameters,
                    keys,
                    nSurroundingAA,
                    linePrefix,
                    peptideMatch,
                    psParameter,
                    peptideFeature,
                    validatedOnly,
                    decoys,
                    waitingHandler));
          }
          writer.newLine();
          if (psmSection != null) {
            String psmSectionPrefix = "";
            if (linePrefix != null) {
              psmSectionPrefix += linePrefix;
            }
            psmSectionPrefix += line + ".";
            writer.increaseDepth();
            if (waitingHandler != null) {
              waitingHandler.setDisplayProgress(false);
            }
            psmSection.writeSection(
                identification,
                identificationFeaturesGenerator,
                identificationParameters,
                peptideMatch.getSpectrumMatchesKeys(),
                psmSectionPrefix,
                nSurroundingAA,
                validatedOnly,
                decoys,
                waitingHandler);
            if (waitingHandler != null) {
              waitingHandler.setDisplayProgress(true);
            }
            writer.decreseDepth();
          }
          line++;
        }
      }
    }
  }
 /**
  * Returns the component of the section corresponding to the given feature.
  *
  * @param identification the identification of the project
  * @param identificationFeaturesGenerator the identification features generator of the project
  * @param identificationParameters the identification parameters
  * @param keys the keys of the protein matches to output
  * @param nSurroundingAA the number of surrounding amino acids to export
  * @param linePrefix the line prefix to use.
  * @param peptideMatch the peptide match
  * @param psParameter the PeptideShaker parameters of the match
  * @param peptideFeature the peptide feature to export
  * @param validatedOnly whether only validated matches should be exported
  * @param decoys whether decoy matches should be exported as well
  * @param waitingHandler the waiting handler
  * @return the component of the section corresponding to the given feature
  * @throws IOException exception thrown whenever an error occurred while interacting with a file
  *     while mapping potential modification sites
  * @throws InterruptedException exception thrown whenever a threading issue occurred while mapping
  *     potential modification sites
  * @throws ClassNotFoundException exception thrown whenever an error occurred while deserializing
  *     an object from the ProteinTree
  * @throws SQLException exception thrown whenever an error occurred while interacting with the
  *     ProteinTree
  * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
  *     occurred while reading an mzML file
  */
 public static String getfeature(
     Identification identification,
     IdentificationFeaturesGenerator identificationFeaturesGenerator,
     IdentificationParameters identificationParameters,
     ArrayList<String> keys,
     int nSurroundingAA,
     String linePrefix,
     PeptideMatch peptideMatch,
     PSParameter psParameter,
     PsPeptideFeature peptideFeature,
     boolean validatedOnly,
     boolean decoys,
     WaitingHandler waitingHandler)
     throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException,
         InterruptedException, MzMLUnmarshallerException {
   switch (peptideFeature) {
     case accessions:
       StringBuilder proteins = new StringBuilder();
       ArrayList<String> accessions =
           peptideMatch
               .getTheoreticPeptide()
               .getParentProteins(identificationParameters.getSequenceMatchingPreferences());
       Collections.sort(accessions);
       for (String accession : accessions) {
         if (proteins.length() > 0) {
           proteins.append("; ");
         }
         proteins.append(accession);
       }
       return proteins.toString();
     case protein_description:
       SequenceFactory sequenceFactory = SequenceFactory.getInstance();
       StringBuilder descriptions = new StringBuilder();
       accessions =
           peptideMatch
               .getTheoreticPeptide()
               .getParentProteins(identificationParameters.getSequenceMatchingPreferences());
       Collections.sort(accessions);
       for (String accession : accessions) {
         if (descriptions.length() > 0) {
           descriptions.append("; ");
         }
         descriptions.append(sequenceFactory.getHeader(accession).getDescription());
       }
       return descriptions.toString();
     case protein_groups:
       HashSet<String> proteinGroups =
           identification.getProteinMatches(peptideMatch.getTheoreticPeptide());
       proteins = new StringBuilder();
       ArrayList<String> proteinGroupsList = new ArrayList<String>(proteinGroups);
       Collections.sort(proteinGroupsList);
       if (proteinGroupsList.size() > 1) {
         identification.loadProteinMatchParameters(
             proteinGroupsList, psParameter, waitingHandler, false);
       }
       psParameter = new PSParameter();
       for (String proteinGroup : proteinGroupsList) {
         if (identification.getProteinIdentification().contains(proteinGroup)) {
           psParameter =
               (PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter);
           if (proteins.length() > 0) {
             proteins.append("; ");
           }
           List<String> groupAccessions = Arrays.asList(ProteinMatch.getAccessions(proteinGroup));
           Collections.sort(groupAccessions);
           boolean first = true;
           for (String accession : groupAccessions) {
             if (first) {
               first = false;
             } else {
               proteins.append(", ");
             }
             proteins.append(accession);
           }
           proteins.append(" (");
           proteins.append(psParameter.getMatchValidationLevel().getName());
           proteins.append(")");
         }
       }
       return proteins.toString();
     case best_protein_group_validation:
       MatchValidationLevel bestProteinValidationLevel = MatchValidationLevel.none;
       proteinGroups = identification.getProteinMatches(peptideMatch.getTheoreticPeptide());
       proteinGroupsList = new ArrayList<String>(proteinGroups);
       Collections.sort(proteinGroupsList);
       if (proteinGroupsList.size() > 1) {
         identification.loadProteinMatchParameters(
             proteinGroupsList, psParameter, waitingHandler, false);
       }
       psParameter = new PSParameter();
       for (String proteinGroup : proteinGroupsList) {
         if (identification.getProteinIdentification().contains(proteinGroup)) {
           psParameter =
               (PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter);
           if (psParameter.getMatchValidationLevel().getIndex()
               > bestProteinValidationLevel.getIndex()) {
             bestProteinValidationLevel = psParameter.getMatchValidationLevel();
           }
         }
       }
       return bestProteinValidationLevel.getName();
     case confidence:
       return psParameter.getPeptideConfidence() + "";
     case decoy:
       if (peptideMatch
           .getTheoreticPeptide()
           .isDecoy(identificationParameters.getSequenceMatchingPreferences())) {
         return "1";
       } else {
         return "0";
       }
     case hidden:
       if (psParameter.isHidden()) {
         return "1";
       } else {
         return "0";
       }
     case localization_confidence:
       return getPeptideModificationLocations(
               peptideMatch, identificationParameters.getSearchParameters().getPtmSettings())
           + "";
     case pi:
       return psParameter.getProteinInferenceClassAsString();
     case position:
       accessions =
           peptideMatch
               .getTheoreticPeptide()
               .getParentProteins(identificationParameters.getSequenceMatchingPreferences());
       Collections.sort(accessions);
       Peptide peptide = peptideMatch.getTheoreticPeptide();
       String start = "";
       for (String proteinAccession : accessions) {
         if (!start.equals("")) {
           start += "; ";
         }
         Protein protein = SequenceFactory.getInstance().getProtein(proteinAccession);
         ArrayList<Integer> starts =
             protein.getPeptideStart(
                 peptide.getSequence(), identificationParameters.getSequenceMatchingPreferences());
         Collections.sort(starts);
         boolean first = true;
         for (int startAa : starts) {
           if (first) {
             first = false;
           } else {
             start += ", ";
           }
           start += startAa;
         }
       }
       return start;
     case psms:
       return peptideMatch.getSpectrumCount() + "";
     case variable_ptms:
       return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), true);
     case fixed_ptms:
       return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), false);
     case score:
       return psParameter.getPeptideScore() + "";
     case raw_score:
       return psParameter.getPeptideProbabilityScore() + "";
     case sequence:
       return peptideMatch.getTheoreticPeptide().getSequence();
     case missed_cleavages:
       peptide = peptideMatch.getTheoreticPeptide();
       Integer nMissedCleavages =
           peptide.getNMissedCleavages(
               identificationParameters.getSearchParameters().getDigestionPreferences());
       if (nMissedCleavages == null) {
         nMissedCleavages = 0;
       }
       return nMissedCleavages + "";
     case modified_sequence:
       return peptideMatch
           .getTheoreticPeptide()
           .getTaggedModifiedSequence(
               identificationParameters.getSearchParameters().getPtmSettings(),
               false,
               false,
               true);
     case starred:
       if (psParameter.isStarred()) {
         return "1";
       } else {
         return "0";
       }
     case aaBefore:
       peptide = peptideMatch.getTheoreticPeptide();
       accessions =
           peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
       Collections.sort(accessions);
       String subSequence = "";
       for (String proteinAccession : accessions) {
         if (!subSequence.equals("")) {
           subSequence += "; ";
         }
         HashMap<Integer, String[]> surroundingAAs =
             SequenceFactory.getInstance()
                 .getProtein(proteinAccession)
                 .getSurroundingAA(
                     peptide.getSequence(),
                     nSurroundingAA,
                     identificationParameters.getSequenceMatchingPreferences());
         ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet());
         Collections.sort(starts);
         boolean first = true;
         for (int startAa : starts) {
           if (first) {
             first = false;
           } else {
             subSequence += ", ";
           }
           subSequence += surroundingAAs.get(startAa)[0];
         }
       }
       return subSequence;
     case aaAfter:
       peptide = peptideMatch.getTheoreticPeptide();
       accessions =
           peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
       Collections.sort(accessions);
       subSequence = "";
       for (String proteinAccession : accessions) {
         if (!subSequence.equals("")) {
           subSequence += "; ";
         }
         HashMap<Integer, String[]> surroundingAAs =
             SequenceFactory.getInstance()
                 .getProtein(proteinAccession)
                 .getSurroundingAA(
                     peptide.getSequence(),
                     nSurroundingAA,
                     identificationParameters.getSequenceMatchingPreferences());
         ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet());
         Collections.sort(starts);
         boolean first = true;
         for (int startAa : starts) {
           if (first) {
             first = false;
           } else {
             subSequence += ", ";
           }
           subSequence += surroundingAAs.get(startAa)[1];
         }
       }
       return subSequence;
     case nValidatedProteinGroups:
       peptide = peptideMatch.getTheoreticPeptide();
       return identificationFeaturesGenerator.getNValidatedProteinGroups(peptide, waitingHandler)
           + "";
     case unique_database:
       peptide = peptideMatch.getTheoreticPeptide();
       if (identification.isUniqueInDatabase(peptide)) {
         return "1";
       } else {
         return "0";
       }
     case validated:
       return psParameter.getMatchValidationLevel().toString();
     case validated_psms:
       return identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideMatch.getKey())
           + "";
     case probabilistic_score:
       PSPtmScores ptmScores = new PSPtmScores();
       ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores);
       if (ptmScores != null) {
         StringBuilder result = new StringBuilder();
         ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
         Collections.sort(modList);
         for (String mod : modList) {
           PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
           ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites());
           if (!sites.isEmpty()) {
             Collections.sort(sites);
             if (result.length() > 0) {
               result.append(", ");
             }
             result.append(mod).append(" (");
             boolean firstSite = true;
             for (int site : sites) {
               if (firstSite) {
                 firstSite = false;
               } else {
                 result.append(", ");
               }
               result.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site));
             }
             result.append(")");
           }
         }
         return result.toString();
       }
       return "";
     case d_score:
       StringBuilder result = new StringBuilder();
       ptmScores = new PSPtmScores();
       ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores);
       if (ptmScores != null) {
         ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
         Collections.sort(modList);
         for (String mod : modList) {
           PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
           ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getDSites());
           if (!sites.isEmpty()) {
             Collections.sort(sites);
             if (result.length() > 0) {
               result.append(", ");
             }
             result.append(mod).append(" (");
             boolean firstSite = true;
             for (int site : sites) {
               if (firstSite) {
                 firstSite = false;
               } else {
                 result.append(", ");
               }
               result.append(site).append(": ").append(ptmScoring.getDeltaScore(site));
             }
             result.append(")");
           }
         }
         return result.toString();
       }
       return "";
     case confident_modification_sites:
       String sequence = peptideMatch.getTheoreticPeptide().getSequence();
       return identificationFeaturesGenerator.getConfidentPtmSites(peptideMatch, sequence);
     case confident_modification_sites_number:
       return identificationFeaturesGenerator.getConfidentPtmSitesNumber(peptideMatch);
     case ambiguous_modification_sites:
       sequence = peptideMatch.getTheoreticPeptide().getSequence();
       return identificationFeaturesGenerator.getAmbiguousPtmSites(peptideMatch, sequence);
     case ambiguous_modification_sites_number:
       return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber(peptideMatch);
     case confident_phosphosites:
       ArrayList<String> modifications = new ArrayList<String>();
       for (String ptm :
           identificationParameters
               .getSearchParameters()
               .getPtmSettings()
               .getAllNotFixedModifications()) {
         if (ptm.contains("Phospho")) {
           modifications.add(ptm);
         }
       }
       return identificationFeaturesGenerator.getConfidentPtmSites(
           peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications);
     case confident_phosphosites_number:
       modifications = new ArrayList<String>();
       for (String ptm :
           identificationParameters
               .getSearchParameters()
               .getPtmSettings()
               .getAllNotFixedModifications()) {
         if (ptm.contains("Phospho")) {
           modifications.add(ptm);
         }
       }
       return identificationFeaturesGenerator.getConfidentPtmSitesNumber(
           peptideMatch, modifications);
     case ambiguous_phosphosites:
       modifications = new ArrayList<String>();
       for (String ptm :
           identificationParameters
               .getSearchParameters()
               .getPtmSettings()
               .getAllNotFixedModifications()) {
         if (ptm.contains("Phospho")) {
           modifications.add(ptm);
         }
       }
       return identificationFeaturesGenerator.getAmbiguousPtmSites(
           peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications);
     case ambiguous_phosphosites_number:
       modifications = new ArrayList<String>();
       for (String ptm :
           identificationParameters
               .getSearchParameters()
               .getPtmSettings()
               .getAllNotFixedModifications()) {
         if (ptm.contains("Phospho")) {
           modifications.add(ptm);
         }
       }
       return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber(
           peptideMatch, modifications);
     default:
       return "Not implemented";
   }
 }
  @Override
  public boolean isValidated(
      String itemName,
      FilterItemComparator filterItemComparator,
      Object value,
      String matchKey,
      Identification identification,
      IdentificationFeaturesGenerator identificationFeaturesGenerator,
      ShotgunProtocol shotgunProtocol,
      IdentificationParameters identificationParameters,
      PeptideSpectrumAnnotator peptideSpectrumAnnotator)
      throws IOException, InterruptedException, ClassNotFoundException, SQLException,
          MzMLUnmarshallerException, MathException {

    PeptideFilterItem filterItem = PeptideFilterItem.getItem(itemName);
    if (filterItem == null) {
      throw new IllegalArgumentException(
          "Filter item " + itemName + "not recognized as peptide filter item.");
    }
    String input = value.toString();
    switch (filterItem) {
      case proteinAccession:
        PeptideMatch peptideMatch = identification.getPeptideMatch(matchKey);
        return filterItemComparator.passes(
            input,
            peptideMatch
                .getTheoreticPeptide()
                .getParentProteins(identificationParameters.getSequenceMatchingPreferences()));
      case proteinDescription:
        peptideMatch = identification.getPeptideMatch(matchKey);
        ArrayList<String> accessions =
            peptideMatch
                .getTheoreticPeptide()
                .getParentProteins(identificationParameters.getSequenceMatchingPreferences());
        ArrayList<String> descriptions = new ArrayList<String>();
        for (String accession : accessions) {
          Header proteinHeader = SequenceFactory.getInstance().getHeader(accession);
          descriptions.add(proteinHeader.getDescription());
        }
        return filterItemComparator.passes(input, descriptions);
      case sequence:
        return filterItemComparator.passes(input, Peptide.getSequence(matchKey));
      case ptm:
        peptideMatch = identification.getPeptideMatch(matchKey);
        ArrayList<String> ptms;
        PSPtmScores psPtmScores = new PSPtmScores();
        psPtmScores = (PSPtmScores) peptideMatch.getUrParam(psPtmScores);
        if (psPtmScores != null) {
          ptms = psPtmScores.getScoredPTMs();
        } else {
          ptms = new ArrayList<String>(0);
        }
        return filterItemComparator.passes(input, ptms);
      case nPSMs:
        peptideMatch = identification.getPeptideMatch(matchKey);
        Integer nPsms = peptideMatch.getSpectrumCount();
        return filterItemComparator.passes(input, nPsms.toString());
      case nValidatedPSMs:
        nPsms = identificationFeaturesGenerator.getNValidatedSpectraForPeptide(matchKey);
        return filterItemComparator.passes(input, nPsms.toString());
      case nConfidentPSMs:
        nPsms = identificationFeaturesGenerator.getNConfidentSpectraForPeptide(matchKey);
        return filterItemComparator.passes(input, nPsms.toString());
      case confidence:
        PSParameter psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
        Double confidence = psParameter.getProteinConfidence();
        return filterItemComparator.passes(input, confidence.toString());
      case proteinInference:
        psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
        Integer pi = psParameter.getProteinInferenceClass();
        return filterItemComparator.passes(input, pi.toString());
      case validationStatus:
        psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
        Integer validation = psParameter.getMatchValidationLevel().getIndex();
        return filterItemComparator.passes(input, validation.toString());
      case stared:
        psParameter = new PSParameter();
        psParameter = (PSParameter) identification.getPeptideMatchParameter(matchKey, psParameter);
        String starred;
        if (psParameter.isStarred()) {
          starred = FilterItemComparator.trueFalse[0];
        } else {
          starred = FilterItemComparator.trueFalse[1];
        }
        return filterItemComparator.passes(input, starred);
      default:
        throw new IllegalArgumentException(
            "Protein filter not implemented for item " + filterItem.name + ".");
    }
  }