Package net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.elements

Examples of net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.elements.ElementRule

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    String elementsArray[] = elements.split(",");
    for (String elementEntry : elementsArray) {

      try {
        ElementRule rule = new ElementRule(elementEntry);

        // We can ignore elements with max 0 atoms
        if (rule.getMaxCount() == 0)
          continue;

        rulesSet.add(rule);

      } catch (IllegalArgumentException e) {
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      String elementsArray[] = elements.split(",");
      for (String elementEntry : elementsArray) {

        try {
          ElementRule rule = new ElementRule(elementEntry);

          // We can ignore elements with max 0 atoms
          if (rule.getMaxCount() == 0) {
            continue;
          }

          // Adjust the maximum numbers according to the mass we are
          // searching
          int maxCountAccordingToMass = (int) (massRange.getMax() / rule
              .getMass());
          if (rule.getMaxCount() > maxCountAccordingToMass) {
            rule.setMaxCount(maxCountAccordingToMass);
          }

          rulesSet.add(rule);

        } catch (IllegalArgumentException e) {
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          + msmsScan.getScanNumber());
    }
    // Sorted by mass in descending order
    ArrayList<ElementRule> rulesSet = new ArrayList<ElementRule>();
    for (IIsotope isotope : parentFormula.isotopes()) {
      ElementRule rule = new ElementRule(isotope.getSymbol(), 0,
          parentFormula.getIsotopeCount(isotope));
      rulesSet.add(rule);
    }
    ElementRule msmsElementRules[] = rulesSet.toArray(new ElementRule[0]);

    int totalMSMSpeaks = 0, interpretedMSMSpeaks = 0;
    Map<DataPoint, String> msmsAnnotations = new Hashtable<DataPoint, String>();

    msmsCycle : for (DataPoint dp : msmsIons) {
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Related Classes of net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.elements.ElementRule

  • net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.SingleRowPredictionTask
  • net.sf.mzmine.modules.peaklistmethods.identification.formulapredictionpeaklist.FormulaPredictionPeakListTask
  • net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScoreCalculator
  • org.openscience.cdk.config.IsotopeFactory
  • org.openscience.cdk.interfaces.IChemObjectBuilder
  • java.util.regex.Pattern
  • java.util.regex.Matcher
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