/**
  * Returns the description of an item.
  *
  * @param key the key of the item
  * @param itemType the type of the item
  * @return the description of an item
  * @throws SQLException thrown if an SQLException occurs
  * @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
  * @throws IOException thrown if an IOException occurs
  * @throws InterruptedException thrown if an InterruptedException occurs
  */
 private String getItemDescription(String key, Type itemType)
     throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException,
         InterruptedException {
   Identification identification = peptideShakerGUI.getIdentification();
   switch (itemType) {
     case PROTEIN:
       ProteinMatch proteinMatch = identification.getProteinMatch(key);
       String mainMatch = proteinMatch.getMainMatch();
       String description = sequenceFactory.getHeader(mainMatch).getSimpleProteinDescription();
       String result = mainMatch;
       for (String accession : ProteinMatch.getAccessions(key)) {
         if (!accession.equals(mainMatch)) {
           if (!result.equals(mainMatch)) {
             result += ", ";
           }
           result += accession;
         }
       }
       result += " - " + description;
       return result;
     case PEPTIDE:
       PeptideMatch peptideMatch = identification.getPeptideMatch(key);
       return peptideShakerGUI
           .getDisplayFeaturesGenerator()
           .getTaggedPeptideSequence(peptideMatch, true, true, true);
     case SPECTRUM:
       return Spectrum.getSpectrumTitle(key) + " (" + Spectrum.getSpectrumFile(key) + ")";
     default:
       return "Unknown";
   }
 }
 /**
  * Returns the desired spectrum.
  *
  * @param spectrumKey the key of the spectrum
  * @return the desired spectrum
  */
 public MSnSpectrum getSpectrum(String spectrumKey) {
   String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
   String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
   try {
     return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
   } catch (Exception e) {
     System.out.println(e.getMessage());
     return null;
   }
 }
 /**
  * Convenience method to match a reporter ion in a spectrum. The charge is assumed to be 1.
  *
  * @param theoreticIon the theoretic ion to look for
  * @param charge the charge of the ion
  * @param spectrum the spectrum
  * @param massTolerance the mass tolerance to use
  * @return a list of all the ion matches
  * @throws java.lang.InterruptedException exception thrown if the thread is interrupted
  */
 public static ArrayList<IonMatch> matchReporterIon(
     Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)
     throws InterruptedException {
   ArrayList<IonMatch> result = new ArrayList<IonMatch>(1);
   double targetMass = theoreticIon.getTheoreticMz(charge);
   for (double mz : spectrum.getOrderedMzValues()) {
     if (Math.abs(mz - targetMass) <= massTolerance) {
       result.add(new IonMatch(spectrum.getPeakMap().get(mz), theoreticIon, charge));
     }
     if (mz > targetMass + massTolerance) {
       break;
     }
   }
   return result;
 }
  /**
   * Indicates whether the match designated by the match key validates the given item using the
   * given comparator and value threshold.
   *
   * @param itemName the name of the item to filter on
   * @param filterItemComparator the comparator to use
   * @param value the value to use as a threshold
   * @param spectrumKey the key of the match of interest
   * @param peptideAssumption the assumption to validate
   * @param identification the identification objects where to get identification matches from
   * @param identificationFeaturesGenerator the identification feature generator where to get
   *     identification features
   * @param identificationParameters the identification parameters used
   * @param peptideSpectrumAnnotator the annotator to use to annotate spectra when filtering on PSM
   *     or assumptions
   * @return a boolean indicating whether the match designated by the protein key validates the
   *     given item using the given comparator and value threshold.
   * @throws java.io.IOException exception thrown whenever an exception occurred while reading or
   *     writing a file
   * @throws java.lang.InterruptedException exception thrown whenever a threading issue occurred
   *     while validating that the match passes the filter
   * @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
   *     deserilalizing a match
   * @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
   *     with a database
   * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
   *     occurred while reading an mzML file
   * @throws org.apache.commons.math.MathException exception thrown whenever an error occurred while
   *     doing statistics on a distribution
   */
  public boolean isValidated(
      String itemName,
      FilterItemComparator filterItemComparator,
      Object value,
      String spectrumKey,
      PeptideAssumption peptideAssumption,
      Identification identification,
      IdentificationFeaturesGenerator identificationFeaturesGenerator,
      IdentificationParameters identificationParameters,
      PeptideSpectrumAnnotator peptideSpectrumAnnotator)
      throws IOException, InterruptedException, ClassNotFoundException, SQLException,
          MzMLUnmarshallerException, MathException {

    AssumptionFilterItem filterItem = AssumptionFilterItem.getItem(itemName);
    if (filterItem == null) {
      throw new IllegalArgumentException(
          "Filter item " + itemName + "not recognized as spectrum assumption filter item.");
    }
    String input = value.toString();
    switch (filterItem) {
      case precrusorMz:
        Precursor precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
        Double mz = precursor.getMz();
        return filterItemComparator.passes(input, mz.toString());
      case precrusorRT:
        precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
        Double rt = precursor.getRt();
        return filterItemComparator.passes(input, rt.toString());
      case precrusorCharge:
        Integer charge = peptideAssumption.getIdentificationCharge().value;
        return filterItemComparator.passes(input, charge.toString());
      case precrusorMzErrorDa:
        precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
        SearchParameters searchParameters = identificationParameters.getSearchParameters();
        Double mzError =
            Math.abs(
                peptideAssumption.getDeltaMass(
                    precursor.getMz(),
                    false,
                    searchParameters.getMinIsotopicCorrection(),
                    searchParameters.getMaxIsotopicCorrection()));
        return filterItemComparator.passes(input, mzError.toString());
      case precrusorMzErrorPpm:
        searchParameters = identificationParameters.getSearchParameters();
        precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
        mzError =
            Math.abs(
                peptideAssumption.getDeltaMass(
                    precursor.getMz(),
                    true,
                    searchParameters.getMinIsotopicCorrection(),
                    searchParameters.getMaxIsotopicCorrection()));
        return filterItemComparator.passes(input, mzError.toString());
      case precrusorMzErrorStat:
        searchParameters = identificationParameters.getSearchParameters();
        precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
        mzError =
            peptideAssumption.getDeltaMass(
                precursor.getMz(),
                identificationParameters.getSearchParameters().isPrecursorAccuracyTypePpm(),
                searchParameters.getMinIsotopicCorrection(),
                searchParameters.getMaxIsotopicCorrection());
        NonSymmetricalNormalDistribution precDeviationDistribution =
            identificationFeaturesGenerator.getMassErrorDistribution(
                Spectrum.getSpectrumFile(spectrumKey));
        Double p;
        if (mzError > precDeviationDistribution.getMean()) {
          p = precDeviationDistribution.getDescendingCumulativeProbabilityAt(mzError);
        } else {
          p = precDeviationDistribution.getCumulativeProbabilityAt(mzError);
        }
        return filterItemComparator.passes(input, p.toString());
      case sequenceCoverage:
        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
        MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
        Peptide peptide = peptideAssumption.getPeptide();
        AnnotationSettings annotationPreferences =
            identificationParameters.getAnnotationPreferences();
        SpecificAnnotationSettings specificAnnotationPreferences =
            annotationPreferences.getSpecificAnnotationPreferences(
                spectrum.getSpectrumKey(),
                peptideAssumption,
                identificationParameters.getSequenceMatchingPreferences(),
                identificationParameters
                    .getPtmScoringPreferences()
                    .getSequenceMatchingPreferences());
        HashMap<Integer, ArrayList<IonMatch>> matches =
            peptideSpectrumAnnotator.getCoveredAminoAcids(
                annotationPreferences,
                specificAnnotationPreferences,
                (MSnSpectrum) spectrum,
                peptide);
        double nCovered = 0;
        int nAA = peptide.getSequence().length();
        for (int i = 0; i <= nAA; i++) {
          ArrayList<IonMatch> matchesAtAa = matches.get(i);
          if (matchesAtAa != null && !matchesAtAa.isEmpty()) {
            nCovered++;
          }
        }
        Double coverage = 100.0 * nCovered / nAA;
        return filterItemComparator.passes(input, coverage.toString());
      case algorithmScore:
        Double score = peptideAssumption.getRawScore();
        if (score == null) {
          score = peptideAssumption.getScore();
        }
        return filterItemComparator.passes(input, score.toString());
      case fileNames:
        return filterItemComparator.passes(input, Spectrum.getSpectrumFile(spectrumKey));
      case confidence:
        PSParameter psParameter = new PSParameter();
        psParameter =
            (PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
        Double confidence = psParameter.getProteinConfidence();
        return filterItemComparator.passes(input, confidence.toString());
      case validationStatus:
        psParameter = new PSParameter();
        psParameter =
            (PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
        Integer validation = psParameter.getMatchValidationLevel().getIndex();
        return filterItemComparator.passes(input, validation.toString());
      case stared:
        psParameter = new PSParameter();
        psParameter =
            (PSParameter) identification.getPeptideMatchParameter(spectrumKey, 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 + ".");
    }
  }