Examples with MergedTandemMassPeak de.ipbhalle.metfraglib.peak.MergedTandemMassPeak used on opensource projects

Example 1 with MergedTandemMassPeak

use of de.ipbhalle.metfraglib.peak.MergedTandemMassPeak in project MetFragRelaunched by ipb-halle.

the class NewMergedPeakFragmenterScore method calculate.

public void calculate() {
    this.matchList = (MatchList) settings.get(VariableNames.MATCH_LIST_NAME);
    this.value = Double.valueOf(0);
    this.bestFragmentIndeces = new int[this.matchList.getNumberElements()];
    this.optimalValues = new double[this.matchList.getNumberElements()];
    for (int i = 0; i < this.matchList.getNumberElements(); i++) {
        DefaultFragmentToPeakMatch currentMatch = null;
        boolean isMatchOfQuerySpectrum = true;
        if (this.matchList.getElement(i) instanceof FragmentMassToPeakMatch)
            currentMatch = (FragmentMassToPeakMatch) this.matchList.getElement(i);
        else
            currentMatch = (FragmentFormulaToPeakMatch) this.matchList.getElement(i);
        double intensity = 0.0;
        try {
            intensity = currentMatch.getMatchedPeak().getIntensity();
        } catch (RelativeIntensityNotDefinedException e) {
            // if the match is not caused by a peak of the query spectrum
            isMatchOfQuerySpectrum = false;
            intensity = 0.0;
        }
        MergedTandemMassPeak matchedPeak = (MergedTandemMassPeak) currentMatch.getMatchedPeak();
        FragmentList currentFragmentList = currentMatch.getMatchedFragmentList();
        double minimumEnergyPerMatch = (double) Integer.MAX_VALUE;
        /*
			 * get all intensities of random spectra of this peak 
			 */
        java.util.ArrayList<Double> intensities = matchedPeak.getIntensities();
        java.util.ArrayList<Integer> spectraIDs = matchedPeak.getSpectraIDs();
        double peakScore = Math.pow((matchedPeak.getMass() / this.measuredPrecursorMass) * 10.0, this.ALPHA) * Math.pow(intensity, this.BETA);
        double[] peakScores = new double[intensities.size()];
        for (int k = 0; k < intensities.size(); k++) {
            peakScores[k] = Math.pow((matchedPeak.getMass() / this.measuredPrecursorMass) * 10.0, this.ALPHA) * Math.pow(intensities.get(k), this.BETA);
        }
        for (int ii = 0; ii < currentFragmentList.getNumberElements(); ii++) {
            IFragment currentFragment = currentFragmentList.getElement(ii);
            /*
				 * check if current fragment is valid based on the tree depth
				 */
            // if(currentFragment.getTreeDepth() > this.maximumTreeDepth) continue;
            int[] brokenBondIndeces = currentFragment.getBrokenBondIndeces();
            double energyOfFragment = 0.0;
            for (int bondIndex : brokenBondIndeces) {
                energyOfFragment += this.bondEnergies[bondIndex];
            }
            energyOfFragment += Math.abs(currentMatch.getNumberOfHydrogensDifferToPeakMass(ii)) * this.WEIGHT_HYDROGEN_PENALTY;
            /*
				 * assign optimal bondenergy and store best fragment
				 */
            if (energyOfFragment < minimumEnergyPerMatch) {
                minimumEnergyPerMatch = energyOfFragment;
                if (isMatchOfQuerySpectrum)
                    this.bestFragmentIndeces[i] = ii;
            }
        }
        if (isMatchOfQuerySpectrum) {
            currentMatch.initialiseBestMatchedFragment(this.bestFragmentIndeces[i]);
            this.value += peakScore / Math.pow(minimumEnergyPerMatch, this.GAMMA);
            this.optimalValues[i] = minimumEnergyPerMatch;
        }
        for (int k = 0; k < spectraIDs.size(); k++) {
            this.scoresRandomSpectra[spectraIDs.get(k)] += peakScores[k] / Math.pow(minimumEnergyPerMatch, this.GAMMA);
        }
    }
    int betterEqualScores = 0;
    for (int i = 0; i < this.scoresRandomSpectra.length; i++) {
        if (this.scoresRandomSpectra[i] >= this.value)
            betterEqualScores++;
    }
    this.scoredCandidate.setProperty("p-value", (double) betterEqualScores / (double) this.scoresRandomSpectra.length);
    this.calculationFinished = true;
}

Example 2 with MergedTandemMassPeak

use of de.ipbhalle.metfraglib.peak.MergedTandemMassPeak in project MetFragRelaunched by ipb-halle.

the class FilteredMergedRandomTandemMassPeakListReader method read.

@Override
public DefaultPeakList read() {
    /*
		 * reading the query peak list
		 */
    SortedTandemMassPeakList peakList = (SortedTandemMassPeakList) super.read();
    /*
		 * generating randomised spectra queried from massbank
		 */
    Double exactMass = (Double) this.settings.get(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME);
    java.util.ArrayList<MergedTandemMassPeak> mergedTandemMassPeaks = new java.util.ArrayList<MergedTandemMassPeak>();
    for (int i = 0; i < peakList.getNumberElements(); i++) {
        MergedTandemMassPeak newMergedTandemMassPeak = new MergedTandemMassPeak(peakList.getElement(i).getMass(), peakList.getElement(i).getAbsoluteIntensity());
        newMergedTandemMassPeak.setRelativeIntensity(peakList.getElement(i).getRelativeIntensity());
        mergedTandemMassPeaks.add(newMergedTandemMassPeak);
    }
    int index = 0;
    for (int i = 0; i < this.numberRandomSpectra; i++) {
        double[][] currentRandomSpectrum = this.generateRandomSpectrum(exactMass, peakList);
        for (int k = 0; k < currentRandomSpectrum.length; k++) {
            index = 0;
            boolean found = false;
            while (index < mergedTandemMassPeaks.size()) {
                if (mergedTandemMassPeaks.get(index).getMass() == currentRandomSpectrum[k][0]) {
                    found = true;
                    break;
                } else if (mergedTandemMassPeaks.get(index).getMass() > currentRandomSpectrum[k][0]) {
                    break;
                }
                index++;
            }
            if (found) {
                mergedTandemMassPeaks.get(index).getIntensities().add(currentRandomSpectrum[k][1]);
                mergedTandemMassPeaks.get(index).getSpectraIDs().add(i);
            } else {
                MergedTandemMassPeak newMergedTandemMassPeak = new MergedTandemMassPeak(currentRandomSpectrum[k][0], -1.0);
                newMergedTandemMassPeak.getIntensities().add(currentRandomSpectrum[k][1]);
                newMergedTandemMassPeak.getSpectraIDs().add(i);
                mergedTandemMassPeaks.add(index, newMergedTandemMassPeak);
            }
        }
    }
    SortedMergedTandemMassPeakList sortedMergedTandemMassPeakList = new SortedMergedTandemMassPeakList(exactMass);
    for (int i = 0; i < mergedTandemMassPeaks.size(); i++) {
        sortedMergedTandemMassPeakList.addElement(mergedTandemMassPeaks.get(i));
    }
    return sortedMergedTandemMassPeakList;
}