Examples with IFragment de.ipbhalle.metfraglib.interfaces.IFragment used on opensource projects

Example 11 with IFragment

use of de.ipbhalle.metfraglib.interfaces.IFragment in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterLossFragmentSmilesPSV method createLossAnnotations.

/**
 * @param matchList
 * @param settings
 * @throws Exception
 */
private String createLossAnnotations(IMolecularStructure precursorMolecule, MatchList matchList, Settings settings, double[] correctedMasses, Fingerprint fingerprint) throws Exception {
    java.util.ArrayList<String> lossFingerprint = new java.util.ArrayList<String>();
    java.util.ArrayList<Double> lossMassDiff = new java.util.ArrayList<Double>();
    // for the precursor ion
    int ionmode = (Integer) settings.get(VariableNames.PRECURSOR_ION_MODE_NAME);
    boolean ispositive = (Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME);
    double adductMass = Constants.getIonisationTypeMassCorrection(Constants.ADDUCT_NOMINAL_MASSES.indexOf(ionmode), ispositive);
    double precursorMass = (Double) settings.get(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME);
    if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
        precursorMass = precursorMolecule.getNeutralMonoisotopicMass();
    double ionmass = MathTools.round(precursorMass + adductMass);
    // check all matches
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        IMatch matchI = matchList.getElement(i);
        IFragment fragmentI = matchI.getBestMatchedFragment();
        double peakMassI = matchI.getMatchedPeak().getMass();
        if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
            peakMassI = correctedMasses[i];
        // compare with matches having greater mass than the current one
        for (int j = i + 1; j < matchList.getNumberElements(); j++) {
            IMatch matchJ = matchList.getElement(j);
            double peakMassJ = matchJ.getMatchedPeak().getMass();
            if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
                peakMassJ = correctedMasses[j];
            IFragment fragmentJ = matchJ.getBestMatchedFragment();
            if (fragmentJ.isRealSubStructure(fragmentI)) {
                double diff = MathTools.round(peakMassJ - peakMassI);
                IFragment diffFragment = fragmentJ.getDifferenceFragment(precursorMolecule, fragmentI);
                if (diffFragment == null)
                    continue;
                IAtomContainer con = fingerprint.getNormalizedAtomContainer(precursorMolecule, diffFragment);
                lossFingerprint.add(fingerprint.getNormalizedFingerprint(con));
                lossMassDiff.add(diff);
            }
        }
        // do the same for the precursor ion
        double diff = MathTools.round(ionmass - peakMassI);
        IFragment diffFragment = fragmentI.getDifferenceFragment(precursorMolecule);
        if (diffFragment == null)
            continue;
        IAtomContainer con = fingerprint.getNormalizedAtomContainer(precursorMolecule, diffFragment);
        lossFingerprint.add(fingerprint.getNormalizedFingerprint(con));
        lossMassDiff.add(diff);
    }
    StringBuilder diffFingerPrint = new StringBuilder();
    if (lossMassDiff.size() >= 1) {
        diffFingerPrint.append(lossMassDiff.get(0));
        diffFingerPrint.append(":");
        diffFingerPrint.append(lossFingerprint.get(0));
    }
    for (int i = 1; i < lossMassDiff.size(); i++) {
        diffFingerPrint.append(";");
        diffFingerPrint.append(lossMassDiff.get(i));
        diffFingerPrint.append(":");
        diffFingerPrint.append(lossFingerprint.get(i));
    }
    return diffFingerPrint.length() == 0 ? "NA" : diffFingerPrint.toString();
}

Example 12 with IFragment

use of de.ipbhalle.metfraglib.interfaces.IFragment in project MetFragRelaunched by ipb-halle.

the class AutomatedPeakFingerprintAnnotationScoreInitialiser method postProcessScoreParameters.

public void postProcessScoreParameters(Settings settings) throws Exception {
    CombinedSingleCandidateMetFragProcess[] processes = (CombinedSingleCandidateMetFragProcess[]) settings.get(VariableNames.METFRAG_PROCESSES_NAME);
    // to determine F_u
    MassToFingerprintsHashMap peakMassToFingerprints = new MassToFingerprintsHashMap();
    MassToFingerprintGroupListCollection peakToFingerprintGroupListCollection = (MassToFingerprintGroupListCollection) settings.get(VariableNames.PEAK_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME);
    Fingerprint fingerprint = new Fingerprint((String) settings.get(VariableNames.FINGERPRINT_TYPE_NAME));
    DefaultPeakList peakList = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    for (CombinedSingleCandidateMetFragProcess scmfp : processes) {
        /*
			 * check whether the single run was successful
			 */
        if (scmfp.wasSuccessful()) {
            ICandidate candidate = scmfp.getScoredPrecursorCandidates()[0];
            MatchList matchlist = candidate.getMatchList();
            java.util.LinkedList<Double> nonExplainedPeaks = this.getNonExplainedPeaks(peakList, matchlist);
            java.util.ArrayList<MassFingerprintMatch> peakMatchlist = new java.util.ArrayList<MassFingerprintMatch>();
            int numberMatchedPeaks = matchlist == null ? 0 : matchlist.getNumberElements();
            candidate.initialisePrecursorCandidate();
            for (int j = 0; j < numberMatchedPeaks + nonExplainedPeaks.size(); j++) {
                FastBitArray currentFingerprint = null;
                Double mass = null;
                // check if it's a valid match (peak-fragment assignment)
                if (j < matchlist.getNumberElements()) {
                    IMatch match = matchlist.getElement(j);
                    mass = match.getMatchedPeak().getMass();
                    IFragment frag = match.getBestMatchedFragment();
                    try {
                        IAtomContainer conPre = fingerprint.getNormalizedAtomContainer(candidate.getPrecursorMolecule(), frag);
                        // IAtomContainer con = MoleculeFunctions.convertImplicitToExplicitHydrogens(conPre);
                        currentFingerprint = fingerprint.getNormalizedFastBitArrayFingerprint(conPre);
                    } catch (InvalidSmilesException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    } catch (CDKException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    }
                } else {
                    // else it must be a non-matched peak
                    mass = nonExplainedPeaks.get(j - matchlist.getNumberElements());
                    currentFingerprint = new FastBitArray("0");
                }
                MassToFingerprintGroupList peakToFingerprintGroupList = peakToFingerprintGroupListCollection.getElementByPeak(mass);
                if (peakToFingerprintGroupList == null)
                    continue;
                peakMatchlist.add(new MassFingerprintMatch(mass, currentFingerprint));
                // check whether fingerprint was observed for current peak mass in the training data
                if (!peakToFingerprintGroupList.containsFingerprint(currentFingerprint)) {
                    // if not add the fingerprint to background by addFingerprint function
                    // addFingerprint checks also whether fingerprint was already added
                    peakMassToFingerprints.addFingerprint(mass, currentFingerprint);
                }
            }
            candidate.setProperty("PeakMatchList", peakMatchlist);
        }
    }
    // f_s
    double f_seen_matched = (double) settings.get(VariableNames.PEAK_FINGERPRINT_MATCHED_TUPLE_COUNT_NAME);
    // f_s
    double f_seen_non_matched = (double) settings.get(VariableNames.PEAK_FINGERPRINT_NON_MATCHED_TUPLE_COUNT_NAME);
    // f_u
    double f_unseen_matched = peakMassToFingerprints.getOverallMatchedSize();
    // f_u
    double f_unseen_non_matched = peakMassToFingerprints.getOverallNonMatchedSize();
    // alpha
    double alpha = (double) settings.get(VariableNames.PEAK_FINGERPRINT_ANNOTATION_ALPHA_VALUE_NAME);
    // beta
    double beta = (double) settings.get(VariableNames.PEAK_FINGERPRINT_ANNOTATION_BETA_VALUE_NAME);
    // \sum_N \sum_Ln 1
    double sumFingerprintFrequencies = (double) settings.get(VariableNames.PEAK_FINGERPRINT_DENOMINATOR_COUNT_NAME);
    // set value for denominator of P(f,m)
    double denominatorValue = sumFingerprintFrequencies + alpha * (f_seen_matched + f_unseen_matched) + beta * (f_seen_non_matched + f_unseen_non_matched);
    settings.set(VariableNames.PEAK_FINGERPRINT_DENOMINATOR_VALUE_NAME, denominatorValue);
    // P(f,m) F_u
    double alphaProbability = alpha / denominatorValue;
    // p(f,m) not annotated
    double betaProbability = beta / denominatorValue;
    for (int i = 0; i < peakToFingerprintGroupListCollection.getNumberElements(); i++) {
        MassToFingerprintGroupList groupList = peakToFingerprintGroupListCollection.getElement(i);
        // sum_f P(f,m)
        // calculate sum of MF_s (including the alpha count) and the joint probabilities
        // at this stage getProbability() returns the absolute counts from the annotation files
        double sum_f = 0.0;
        double sumFsProbabilities = 0.0;
        for (int ii = 0; ii < groupList.getNumberElements(); ii++) {
            // first calculate P(f,m)
            if (groupList.getElement(ii).getFingerprint().getSize() != 1)
                groupList.getElement(ii).setJointProbability((groupList.getElement(ii).getProbability() + alpha) / denominatorValue);
            else
                groupList.getElement(ii).setJointProbability((groupList.getElement(ii).getProbability() + beta) / denominatorValue);
            // sum_f P(f,m) -> for F_s
            sumFsProbabilities += groupList.getElement(ii).getJointProbability();
        }
        // calculate the sum of probabilities for un-observed fingerprints for the current mass
        double sumFuProbabilities = alphaProbability * peakMassToFingerprints.getSizeMatched(groupList.getPeakmz());
        sumFuProbabilities += betaProbability;
        sum_f += sumFsProbabilities;
        sum_f += sumFuProbabilities;
        for (int ii = 0; ii < groupList.getNumberElements(); ii++) {
            // second calculate P(f|m)
            groupList.getElement(ii).setConditionalProbability_sp(groupList.getElement(ii).getJointProbability() / sum_f);
        }
        groupList.setAlphaProb(alphaProbability / sum_f);
        groupList.setBetaProb(betaProbability / sum_f);
        groupList.setProbabilityToConditionalProbability_sp();
        groupList.calculateSumProbabilites();
    }
    return;
}

Example 13 with IFragment

use of de.ipbhalle.metfraglib.interfaces.IFragment in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterLossFragmentSmilesCompletePSV method createLossAnnotations.

/**
 * @param matchList
 * @param settings
 * @throws Exception
 */
private String[][] createLossAnnotations(IMolecularStructure precursorMolecule, MatchList matchList, Settings settings, double[] correctedMasses, FingerprintCollection fingerprintCollection, java.util.ArrayList<Double> uncorrectedMassDiff) throws Exception {
    java.util.ArrayList<String[]> lossFingerprint = new java.util.ArrayList<String[]>();
    java.util.ArrayList<Double> lossMassDiff = new java.util.ArrayList<Double>();
    // for the precursor ion
    int ionmode = (Integer) settings.get(VariableNames.PRECURSOR_ION_MODE_NAME);
    boolean ispositive = (Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME);
    double adductMass = Constants.getIonisationTypeMassCorrection(Constants.ADDUCT_NOMINAL_MASSES.indexOf(ionmode), ispositive);
    double precursorMass = (Double) settings.get(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME);
    double uncorrectedPrecursorMass = precursorMass;
    if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
        precursorMass = precursorMolecule.getNeutralMonoisotopicMass();
    double ionmass = MathTools.round(precursorMass + adductMass);
    double uncorrectedIonmass = MathTools.round(uncorrectedPrecursorMass + adductMass);
    // check all matches
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        IMatch matchI = matchList.getElement(i);
        IFragment fragmentI = matchI.getBestMatchedFragment();
        double peakMassI = matchI.getMatchedPeak().getMass();
        double uncorrectedPeakMassI = peakMassI;
        if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
            peakMassI = correctedMasses[i];
        // compare with matches with greater mass than the current one
        for (int j = i + 1; j < matchList.getNumberElements(); j++) {
            IMatch matchJ = matchList.getElement(j);
            double peakMassJ = matchJ.getMatchedPeak().getMass();
            double uncorrectedPeakMassJ = peakMassJ;
            if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME))
                peakMassJ = correctedMasses[j];
            IFragment fragmentJ = matchJ.getBestMatchedFragment();
            if (fragmentJ.isRealSubStructure(fragmentI)) {
                double diff = MathTools.round(peakMassJ - peakMassI);
                double uncorrectedDiff = MathTools.round(uncorrectedPeakMassJ - uncorrectedPeakMassI);
                IFragment diffFragment = fragmentJ.getDifferenceFragment(precursorMolecule, fragmentI);
                if (diffFragment == null)
                    continue;
                IAtomContainer con = fingerprintCollection.getNormalizedAtomContainer(precursorMolecule, diffFragment);
                lossFingerprint.add(fingerprintCollection.getNormalizedFingerprint(con));
                lossMassDiff.add(diff);
                uncorrectedMassDiff.add(uncorrectedDiff);
            }
        }
        // do the same for the precursor ion
        double diff = MathTools.round(ionmass - peakMassI);
        double uncorrectedDiff = MathTools.round(uncorrectedIonmass - uncorrectedPeakMassI);
        IFragment diffFragment = fragmentI.getDifferenceFragment(precursorMolecule);
        if (diffFragment == null)
            continue;
        IAtomContainer con = fingerprintCollection.getNormalizedAtomContainer(precursorMolecule, diffFragment);
        lossFingerprint.add(fingerprintCollection.getNormalizedFingerprint(con));
        lossMassDiff.add(diff);
        uncorrectedMassDiff.add(uncorrectedDiff);
    }
    StringBuilder[] diffFingerPrints = new StringBuilder[fingerprintCollection.getNumberFingerprinters()];
    for (int i = 0; i < diffFingerPrints.length; i++) diffFingerPrints[i] = new StringBuilder();
    if (lossMassDiff.size() >= 1) {
        for (int ii = 0; ii < diffFingerPrints.length; ii++) {
            diffFingerPrints[ii].append(lossMassDiff.get(0));
            diffFingerPrints[ii].append(":");
            diffFingerPrints[ii].append(lossFingerprint.get(0)[ii]);
        }
    }
    for (int i = 1; i < lossMassDiff.size(); i++) {
        for (int ii = 0; ii < diffFingerPrints.length; ii++) {
            diffFingerPrints[ii].append(";");
            diffFingerPrints[ii].append(lossMassDiff.get(i));
            diffFingerPrints[ii].append(":");
            diffFingerPrints[ii].append(lossFingerprint.get(i)[ii]);
        }
    }
    String[][] fps_return = new String[fingerprintCollection.getNumberFingerprinters()][3];
    for (int i = 0; i < fingerprintCollection.getNumberFingerprinters(); i++) {
        if (diffFingerPrints[i].toString().equals(""))
            fps_return[i] = new String[] { "NA", "NA", "NA" };
        else
            fps_return[i] = new String[] { diffFingerPrints[i].toString() };
    }
    return fps_return;
}

Example 14 with IFragment

use of de.ipbhalle.metfraglib.interfaces.IFragment in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterLossFragmentSmilesCompletePSV method writeFile.

public boolean writeFile(File file, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    DefaultPeakList peakList = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    java.io.BufferedWriter bwriter = new BufferedWriter(new FileWriter(file));
    StringBuilder heading = new StringBuilder();
    candidateList.getElement(0).removeProperty("ExplPeaks");
    candidateList.getElement(0).removeProperty("FormulasOfExplPeaks");
    candidateList.getElement(0).removeProperty("NumberPeaksUsed");
    candidateList.getElement(0).removeProperty("NoExplPeaks");
    String[] fpnames = ClassNames.getFingerprintNames();
    for (int ii = 0; ii < fpnames.length; ii++) {
        candidateList.getElement(0).removeProperty("FragmentFingerprintOfExplPeaks" + fpnames[ii]);
        candidateList.getElement(0).removeProperty("LossFingerprintOfExplPeaks" + fpnames[ii]);
    }
    java.util.Enumeration<String> keys = candidateList.getElement(0).getProperties().keys();
    if (keys.hasMoreElements()) {
        String key = keys.nextElement();
        heading.append(key);
    }
    while (keys.hasMoreElements()) {
        String key = keys.nextElement();
        heading.append("|");
        heading.append(key);
    }
    heading.append("|");
    heading.append("ExplPeaks");
    heading.append("|");
    heading.append("FormulasOfExplPeaks");
    heading.append("|");
    heading.append("NumberPeaksUsed");
    heading.append("|");
    heading.append("NoExplPeaks");
    for (int i = 0; i < fpnames.length; i++) {
        heading.append("|");
        heading.append("FragmentFingerprintOfExplPeaks" + fpnames[i]);
        heading.append("|");
        heading.append("LossFingerprintOfExplPeaks" + fpnames[i]);
    }
    heading.append("|");
    heading.append("NonExplainedPeaks");
    heading.append("|");
    heading.append("NonExplainedLosses");
    bwriter.write(heading.toString());
    bwriter.newLine();
    FingerprintCollection fingerprintCollection = new FingerprintCollection();
    int ionmode = (Integer) settings.get(VariableNames.PRECURSOR_ION_MODE_NAME);
    boolean ispositive = (Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME);
    java.util.ArrayList<Double> nativeLossMasses = this.calculatePeakDifferences(peakList, (Double) settings.get(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME), Constants.getIonisationTypeMassCorrection(Constants.ADDUCT_NOMINAL_MASSES.indexOf(ionmode), ispositive));
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        StringBuilder line = new StringBuilder();
        int countExplainedPeaks = 0;
        ICandidate scoredCandidate = candidateList.getElement(i);
        scoredCandidate.removeProperty("ExplPeaks");
        scoredCandidate.removeProperty("FormulasOfExplPeaks");
        scoredCandidate.removeProperty("NumberPeaksUsed");
        scoredCandidate.removeProperty("NoExplPeaks");
        for (int ii = 0; ii < fpnames.length; ii++) {
            scoredCandidate.removeProperty("FragmentFingerprintOfExplPeaks" + fpnames[ii]);
            scoredCandidate.removeProperty("LossFingerprintOfExplPeaks" + fpnames[ii]);
        }
        scoredCandidate.removeProperty("NonExplainedPeaks");
        scoredCandidate.removeProperty("NonExplainedLosses");
        if (settings != null)
            scoredCandidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        scoredCandidate.initialisePrecursorCandidate();
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
        }
        StringBuilder peaksExplained = new StringBuilder();
        StringBuilder sumFormulasOfFragmentsExplainedPeaks = new StringBuilder();
        StringBuilder[] fingerprintOfFragmentsExplainedPeaks = new StringBuilder[fingerprintCollection.getNumberFingerprinters()];
        for (int ii = 0; ii < fingerprintOfFragmentsExplainedPeaks.length; ii++) fingerprintOfFragmentsExplainedPeaks[ii] = new StringBuilder();
        keys = scoredCandidate.getProperties().keys();
        if (keys.hasMoreElements()) {
            String key = keys.nextElement();
            line.append(scoredCandidate.getProperty(key));
        }
        while (keys.hasMoreElements()) {
            String key = keys.nextElement();
            line.append("|");
            line.append(scoredCandidate.getProperty(key));
        }
        if (scoredCandidate.getMatchList() != null) {
            String[] matchedFormulas = new String[scoredCandidate.getMatchList().getNumberElements()];
            double[] correctedMasses = new double[scoredCandidate.getMatchList().getNumberElements()];
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained.append(scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass());
                    peaksExplained.append("_");
                    peaksExplained.append(intensity);
                    peaksExplained.append(";");
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                double mass = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass();
                if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME)) {
                    matchedFormulas[ii] = formula;
                    correctedMasses[ii] = MathTools.round(calculateMassOfFormula(formula));
                    mass = correctedMasses[ii];
                }
                sumFormulasOfFragmentsExplainedPeaks.append(scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass());
                sumFormulasOfFragmentsExplainedPeaks.append(":");
                sumFormulasOfFragmentsExplainedPeaks.append(formula);
                sumFormulasOfFragmentsExplainedPeaks.append(";");
                // get fragment of explained peak
                IFragment frag = scoredCandidate.getMatchList().getElement(ii).getBestMatchedFragment();
                String[] fps = null;
                try {
                    IAtomContainer con = fingerprintCollection.getNormalizedAtomContainer(scoredCandidate.getPrecursorMolecule(), frag);
                    fps = fingerprintCollection.getNormalizedFingerprint(con);
                } catch (Exception e) {
                    continue;
                }
                for (int iii = 0; iii < fps.length; iii++) {
                    fingerprintOfFragmentsExplainedPeaks[iii].append(mass);
                    fingerprintOfFragmentsExplainedPeaks[iii].append(":");
                    fingerprintOfFragmentsExplainedPeaks[iii].append(fps[iii]);
                    fingerprintOfFragmentsExplainedPeaks[iii].append(";");
                }
            }
            line.append("|");
            line.append(peaksExplained.length() == 0 ? "NA" : peaksExplained.substring(0, peaksExplained.length() - 1));
            line.append("|");
            line.append(sumFormulasOfFragmentsExplainedPeaks.length() == 0 ? "NA" : sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1));
            line.append("|");
            line.append(numberOfPeaksUsed);
            line.append("|");
            line.append(countExplainedPeaks);
            java.util.ArrayList<Double> uncorrectedLossMasses = new java.util.ArrayList<Double>();
            // add loss information
            if (settings != null) {
                String[][] lossesInformation = createLossAnnotations(scoredCandidate.getPrecursorMolecule(), scoredCandidate.getMatchList(), settings, correctedMasses, fingerprintCollection, uncorrectedLossMasses);
                for (int ii = 0; ii < fingerprintCollection.getNumberFingerprinters(); ii++) {
                    line.append("|");
                    line.append(fingerprintOfFragmentsExplainedPeaks[ii].length() == 0 ? "NA" : fingerprintOfFragmentsExplainedPeaks[ii].substring(0, fingerprintOfFragmentsExplainedPeaks[ii].length() - 1));
                    line.append("|");
                    line.append(lossesInformation[ii][0]);
                }
            }
            line.append("|");
            line.append(this.getNonExplainedPeakString(peakList, scoredCandidate.getMatchList()));
            line.append("|");
            line.append(this.getNonExplainedLossString(uncorrectedLossMasses, nativeLossMasses));
        }
        bwriter.write(line.toString());
        bwriter.newLine();
    }
    bwriter.close();
    return true;
}

Example 15 with IFragment

use of de.ipbhalle.metfraglib.interfaces.IFragment in project MetFragRelaunched by ipb-halle.

the class HDFragmentPairScore2 method checkForMatchingFragments.

/**
 * @param fragmentList
 * @param fragmentListHD
 * @param deuteriumShift
 * @return
 */
private boolean checkForMatchingFragments(MatchFragmentList fragmentList, MatchFragmentList fragmentListHD, int deuteriumShift) {
    MatchFragmentNode node = fragmentList.getRootNode();
    MatchFragmentNode nodeHD = fragmentListHD.getRootNode();
    while (node != null) {
        while (nodeHD != null) {
            for (int i = 0; i < node.getMatch().getMatchedFragmentsSize(); i++) {
                HDFragmentMassToPeakMatch matchHD = ((HDFragmentMassToPeakMatch) nodeHD.getMatch());
                int numberMatchedFragmentsHD = matchHD.getMatchedFragmentsSize();
                for (int j = 0; j < numberMatchedFragmentsHD; j++) {
                    int numberDeuteriumsOfMatchedFragment = 0;
                    int deuteriumsOfMatchedFragment = matchHD.getNumberOfDeuteriumsOfMatchedFragment(j);
                    int deuteriumDifferenceOfMatchedFragment = matchHD.getNumberOfDeuteriumDifferToPeakMass(j);
                    int deuteriumFromCharge = 0;
                    if (Constants.ADDUCT_NOMINAL_MASSES.get(matchHD.getFragmentsAdductTypeIndex(j)) == 2)
                        deuteriumFromCharge = 1;
                    else if (Constants.ADDUCT_NOMINAL_MASSES.get(matchHD.getFragmentsAdductTypeIndex(j)) == -2)
                        deuteriumFromCharge = -1;
                    numberDeuteriumsOfMatchedFragment = deuteriumsOfMatchedFragment + deuteriumDifferenceOfMatchedFragment + deuteriumFromCharge;
                    IFragment fragment = node.getMatch().getMatchedFragmentList().getElement(i);
                    IFragment fragmentHD = nodeHD.getMatch().getMatchedFragmentList().getElement(j);
                    // if(fragment.equals(fragmentHD) && numberDeuteriumsOfMatchedFragment == deuteriumShift) return true;
                    if (fragment.equals(fragmentHD)) {
                        if (numberDeuteriumsOfMatchedFragment == deuteriumShift)
                            return true;
                        else if ((numberDeuteriumsOfMatchedFragment - deuteriumFromCharge) == deuteriumShift)
                            return true;
                    }
                }
            }
            nodeHD = nodeHD.getNext();
        }
        node = node.getNext();
    }
    return false;
}