Examples with MatchPeakList de.ipbhalle.metfraglib.match.MatchPeakList used on opensource projects

Example 1 with MatchPeakList

use of de.ipbhalle.metfraglib.match.MatchPeakList in project MetFragRelaunched by ipb-halle.

the class HDTopDownFragmenterAssignerScorer method matchFragmentHD.

/**
 * @param tempPeakPointer
 * @param currentFragmentWrapper
 * @param tandemMassPeakList
 * @param sortedScoredPeaks
 * @param newToProcessFragments
 * @param peakIndexToPeakMatch
 * @param fragmentIndexToPeakMatch
 * @return
 */
protected boolean matchFragmentHD(int tempPeakPointer, HDTopDownBitArrayFragmentWrapper currentFragmentWrapper, SortedTandemMassPeakList tandemMassPeakList, java.util.HashMap<Integer, MatchFragmentList> peakIndexToPeakMatch, java.util.HashMap<Integer, MatchPeakList> fragmentIndexToPeakMatch, int precursorIndex) {
    byte matched = -1;
    boolean matchedAndAdded = false;
    while (matched != 1 && tempPeakPointer >= 0) {
        IMatch[] match = new IMatch[1];
        TandemMassPeak currentPeak = tandemMassPeakList.getElement(tempPeakPointer);
        /*
			 * calculate match
			 */
        if (tempPeakPointer >= 0)
            matched = currentFragmentWrapper.matchToPeak(this.candidates[0].getPrecursorMolecule(), currentPeak, this.precursorIonTypeIndexHD, this.positiveMode, match);
        /*
			 * check whether match has occurred
			 */
        if (matched == 0) {
            matchedAndAdded = true;
            currentFragmentWrapper.getWrappedFragment().setPrecursorFragments(true);
            Double[][] currentScores = this.scoreCollection.calculateSingleMatch(match[0]);
            /*
				 * insert fragment into peak's fragment list 
				 */
            /*
				 * first generate the new fragment node and set the score values
				 */
            MatchFragmentNode newNode = new MatchFragmentNode(match[0]);
            newNode.setScore(currentScores[0][0]);
            newNode.setFragmentScores(currentScores[0]);
            newNode.setOptimalValues(currentScores[1]);
            /*
				 * find correct location in the fragment list
				 */
            boolean similarFragmentFound = false;
            if (peakIndexToPeakMatch.containsKey(tempPeakPointer)) {
                Double[] values = peakIndexToPeakMatch.get(tempPeakPointer).containsByFingerprint(currentFragmentWrapper.getWrappedFragment().getAtomsFastBitArray());
                if (values == null) {
                    peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                } else {
                    if (values[0] < currentScores[0][0]) {
                        peakIndexToPeakMatch.get(tempPeakPointer).removeElementByID((int) Math.floor(values[1]));
                        fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).removeElementByID(tempPeakPointer);
                        if (fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).getRootNode() == null) {
                            fragmentIndexToPeakMatch.remove((int) Math.floor(values[1]));
                        }
                        peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                    } else
                        similarFragmentFound = true;
                }
            } else {
                MatchFragmentList newFragmentList = new MatchFragmentList(newNode);
                peakIndexToPeakMatch.put(tempPeakPointer, newFragmentList);
            }
            /*
				 * insert peak into fragment's peak list 
				 */
            if (!similarFragmentFound) {
                if (fragmentIndexToPeakMatch.containsKey(currentFragmentWrapper.getWrappedFragment().getID())) {
                    fragmentIndexToPeakMatch.get(currentFragmentWrapper.getWrappedFragment().getID()).insert(currentPeak, currentScores[0][0], tempPeakPointer);
                } else {
                    MatchPeakList newPeakList = new MatchPeakList(currentPeak, currentScores[0][0], tempPeakPointer);
                    fragmentIndexToPeakMatch.put(currentFragmentWrapper.getWrappedFragment().getID(), newPeakList);
                }
            }
        }
        /*
			 * if the mass of the current fragment was greater than the peak mass then assign the current peak ID to the peak IDs of the
			 * child fragments as they have smaller masses 
			 */
        if (matched == 1 || tempPeakPointer == 0) {
            /*
				 * mark current fragment for further fragmentation
				 */
            currentFragmentWrapper.setCurrentPeakIndexPointerHD(tempPeakPointer);
        }
        /*
			 * if the current fragment has matched to the current peak then set the current peak index to the next peak as the current fragment can 
			 * also match to the next peak
			 * if the current fragment mass was smaller than that of the current peak then set the current peak index to the next peak (reduce the index) 
			 * as the next peak mass is smaller and could match the current smaller fragment mass 
			 */
        if (matched == 0 || matched == -1)
            tempPeakPointer--;
    }
    return matchedAndAdded;
}

Example 2 with MatchPeakList

use of de.ipbhalle.metfraglib.match.MatchPeakList in project MetFragRelaunched by ipb-halle.

the class HDTopDownFragmenterAssignerScorer method calculate.

@Override
@SuppressWarnings("unchecked")
public void calculate() {
    HDTopDownBitArrayPrecursor candidatePrecursor = (HDTopDownBitArrayPrecursor) (this.candidates[0]).getPrecursorMolecule();
    // one native candidate can have multiple deuterated precursors
    int deuteratedCandidateNumber = candidatePrecursor.getNumberDeuteratedCombinations();
    /*
		 * generate root fragment
		 */
    AbstractTopDownBitArrayFragment root = candidatePrecursor.toFragment();
    Byte maximumTreeDepth = (Byte) settings.get(VariableNames.MAXIMUM_TREE_DEPTH_NAME);
    if (maximumTreeDepth == 0) {
        maximumTreeDepth = candidatePrecursor.getNumNodeDegreeOne() >= 4 ? (byte) 3 : (byte) 2;
    }
    this.candidates[0].setProperty(VariableNames.MAXIMUM_TREE_DEPTH_NAME, maximumTreeDepth);
    // native spectrum
    SortedTandemMassPeakList tandemMassPeakList = (SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    tandemMassPeakList.initialiseMassLimits((Double) settings.get(VariableNames.RELATIVE_MASS_DEVIATION_NAME), (Double) settings.get(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME));
    // hd spectrum
    SortedTandemMassPeakList tandemMassPeakListHD = (SortedTandemMassPeakList) settings.get(VariableNames.HD_PEAK_LIST_NAME);
    tandemMassPeakListHD.initialiseMassLimits((Double) settings.get(VariableNames.RELATIVE_MASS_DEVIATION_NAME), (Double) settings.get(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME));
    // native ion type
    Integer precursorIonType = (Integer) settings.get(VariableNames.PRECURSOR_ION_MODE_NAME);
    this.positiveMode = (Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME);
    this.precursorIonTypeIndex = Constants.ADDUCT_NOMINAL_MASSES.indexOf(precursorIonType);
    // hd ion type
    Integer precursorIonTypeHD = (Integer) settings.get(VariableNames.HD_PRECURSOR_ION_MODE_NAME);
    this.precursorIonTypeIndexHD = Constants.ADDUCT_NOMINAL_MASSES.indexOf(precursorIonTypeHD);
    // set the minimum mass limit for fragment generation
    double minimumMassNative = tandemMassPeakList.getMinimumMassValue();
    double minimumMassHD = tandemMassPeakListHD.getMinimumMassValue();
    double minimumMass = minimumMassHD < minimumMassNative ? minimumMassHD : minimumMassNative;
    this.fragmenter.setMinimumFragmentMassLimit(minimumMass - Math.max(Constants.ADDUCT_MASSES.get(precursorIonTypeIndex), Constants.ADDUCT_MASSES.get(precursorIonTypeIndexHD)));
    /*
		 * prepare the processing
		 */
    java.util.Queue<HDTopDownBitArrayFragmentWrapper> toProcessFragments = new java.util.LinkedList<HDTopDownBitArrayFragmentWrapper>();
    /*
		 * wrap the root fragment
		 */
    int[] currentPeakIndexPointerArrayHD = new int[deuteratedCandidateNumber];
    for (int i = 0; i < currentPeakIndexPointerArrayHD.length; i++) currentPeakIndexPointerArrayHD[i] = tandemMassPeakListHD.getNumberElements() - 1;
    HDTopDownBitArrayFragmentWrapper rootFragmentWrapper = new HDTopDownBitArrayFragmentWrapper(root, tandemMassPeakList.getNumberElements() - 1, currentPeakIndexPointerArrayHD);
    toProcessFragments.add(rootFragmentWrapper);
    /*
		 * define the match lists
		 */
    java.util.HashMap<Integer, MatchFragmentList> peakIndexToPeakMatch = new java.util.HashMap<Integer, MatchFragmentList>();
    java.util.HashMap<Integer, MatchPeakList> fragmentIndexToPeakMatch = new java.util.HashMap<Integer, MatchPeakList>();
    java.util.HashMap<Integer, MatchFragmentList>[] peakIndexToPeakMatchHD = new java.util.HashMap[deuteratedCandidateNumber];
    java.util.HashMap<Integer, MatchPeakList>[] fragmentIndexToPeakMatchHD = new java.util.HashMap[deuteratedCandidateNumber];
    for (int i = 0; i < deuteratedCandidateNumber; i++) {
        peakIndexToPeakMatchHD[i] = new java.util.HashMap<Integer, MatchFragmentList>();
        fragmentIndexToPeakMatchHD[i] = new java.util.HashMap<Integer, MatchPeakList>();
    }
    /*
		 * iterate over the maximal allowed tree depth
		 */
    for (int k = 1; k <= maximumTreeDepth; k++) {
        java.util.Queue<HDTopDownBitArrayFragmentWrapper> newToProcessFragments = new java.util.LinkedList<HDTopDownBitArrayFragmentWrapper>();
        /*
			 * use each fragment that is marked as to be processed
			 */
        while (!toProcessFragments.isEmpty()) {
            /*
				 * generate fragments of new tree depth
				 */
            HDTopDownBitArrayFragmentWrapper wrappedPrecursorFragment = toProcessFragments.poll();
            if (wrappedPrecursorFragment.getWrappedFragment().isDiscardedForFragmentation()) {
                AbstractTopDownBitArrayFragment clonedFragment = (AbstractTopDownBitArrayFragment) wrappedPrecursorFragment.getWrappedFragment().clone(this.candidates[0].getPrecursorMolecule());
                clonedFragment.setAsDiscardedForFragmentation();
                newToProcessFragments.add(new HDTopDownBitArrayFragmentWrapper(clonedFragment, wrappedPrecursorFragment.getCurrentPeakIndexPointer(), wrappedPrecursorFragment.getCurrentPeakIndexPointerHD()));
                continue;
            }
            /*
				 * generate fragments of next tree depth
				 */
            java.util.ArrayList<AbstractTopDownBitArrayFragment> fragmentsOfCurrentTreeDepth = this.fragmenter.getFragmentsOfNextTreeDepth(wrappedPrecursorFragment.getWrappedFragment());
            /*
				 * get peak pointer of current precursor fragment
				 */
            int currentPeakPointer = wrappedPrecursorFragment.getCurrentPeakIndexPointer();
            int[] currentPeakPointerHD = wrappedPrecursorFragment.getCurrentPeakIndexPointerArrayHD();
            /*
				 * start loop over all child fragments from precursor fragment
				 * to try assigning them to the current peak
				 */
            for (int l = 0; l < fragmentsOfCurrentTreeDepth.size(); l++) {
                AbstractTopDownBitArrayFragment currentFragment = fragmentsOfCurrentTreeDepth.get(l);
                HDTopDownBitArrayFragmentWrapper newFragmentWrapper = new HDTopDownBitArrayFragmentWrapper(currentFragment, currentPeakPointer, currentPeakPointerHD.clone());
                if (!fragmentsOfCurrentTreeDepth.get(l).isValidFragment()) {
                    newToProcessFragments.add(newFragmentWrapper);
                    continue;
                }
                /*
					 * needs to be set
					 * otherwise you get fragments generated by multiple cleavage in one chain
					 */
                if (this.wasAlreadyGeneratedByHashtable(currentFragment)) {
                    currentFragment.setAsDiscardedForFragmentation();
                    newToProcessFragments.add(newFragmentWrapper);
                    continue;
                }
                int tempPeakPointer = currentPeakPointer;
                this.matchFragment(tempPeakPointer, newFragmentWrapper, tandemMassPeakList, peakIndexToPeakMatch, fragmentIndexToPeakMatch);
                // run over all deuterated combinations
                for (int d = 0; d < deuteratedCandidateNumber; d++) {
                    newFragmentWrapper.setPrecursorIndex(d);
                    int tempPeakPointerHD = newFragmentWrapper.getCurrentPeakIndexPointerHD();
                    this.matchFragmentHD(tempPeakPointerHD, newFragmentWrapper, tandemMassPeakListHD, peakIndexToPeakMatchHD[d], fragmentIndexToPeakMatchHD[d], d);
                }
                newToProcessFragments.add(newFragmentWrapper);
            }
        }
        toProcessFragments = newToProcessFragments;
    }
    this.matchList = new MatchList();
    /*
		 * collect score of all scores over all matches
		 */
    double[][] singleScores = new double[this.scoreCollection.getNumberScores()][peakIndexToPeakMatch.size()];
    java.util.ArrayList<double[][]> singleScoresHD = new java.util.ArrayList<double[][]>();
    for (int d = 0; d < deuteratedCandidateNumber; d++) singleScoresHD.add(new double[this.scoreCollection.getNumberScores()][peakIndexToPeakMatchHD[d].size()]);
    /*
		 * collect the sum of all scores over all matches
		 */
    double[] summedScores = new double[this.scoreCollection.getNumberScores()];
    double[][] summedScoresHD = new double[deuteratedCandidateNumber][this.scoreCollection.getNumberScores()];
    ICandidate[] deuteratedCandidates = new ICandidate[deuteratedCandidateNumber];
    deuteratedCandidates[0] = this.candidates[0];
    for (int i = 1; i < deuteratedCandidateNumber; i++) {
        deuteratedCandidates[i] = new TopDownPrecursorCandidate(this.candidates[0].getInChI(), this.candidates[0].getIdentifier());
        deuteratedCandidates[i].setPrecursorMolecule(candidatePrecursor);
    }
    this.calculateFragmenterScores(peakIndexToPeakMatch, singleScores, summedScores);
    for (int d = 0; d < deuteratedCandidateNumber; d++) {
        this.calculateFragmenterScoresHD(peakIndexToPeakMatchHD[d], singleScoresHD.get(d), summedScoresHD[d], deuteratedCandidates[d], d);
    }
    this.settings.set(VariableNames.PEAK_INDEX_TO_PEAK_MATCH_NAME, peakIndexToPeakMatch);
    this.settings.set(VariableNames.HD_PEAK_INDEX_TO_PEAK_MATCH_NAME, peakIndexToPeakMatchHD[0]);
    this.settings.set(VariableNames.CANDIDATE_NAME, this.candidates[0]);
    this.candidates[0].setMatchList(this.matchList);
    if (this.scoreCollection == null)
        return;
    try {
        for (int i = 0; i < this.scoreCollection.getNumberScores(); i++) {
            if (!this.scoreCollection.getScore(i).calculationFinished()) {
                this.scoreCollection.getScore(i).calculate();
            } else {
                this.scoreCollection.getScore(i).setValue(summedScores[i] + summedScoresHD[0][i]);
            }
            if (singleScores[i].length != 0 && this.scoreCollection.getScore(i).hasInterimResults() && !this.scoreCollection.getScore(i).isInterimResultsCalculated()) {
                this.scoreCollection.getScore(i).setOptimalValues(singleScores[i]);
            }
        }
        // set score values directly for the first candidate only
        String[] score_types = (String[]) this.settings.get(VariableNames.METFRAG_SCORE_TYPES_NAME);
        for (int i = 0; i < score_types.length; i++) {
            if (scoreCollection.getScore(i).getValue() != null) {
                if (!scoreCollection.getScore(i).isUserDefinedPropertyScore()) {
                    this.candidates[0].setProperty(score_types[i], scoreCollection.getScore(i).getValue());
                }
                if (scoreCollection.getScore(i).hasInterimResults()) {
                    this.candidates[0].setProperty(score_types[i] + "_Values", scoreCollection.getScore(i).getOptimalValuesToString());
                }
            }
        }
        // set scores for additional deuterated candidates
        for (int d = 1; d < deuteratedCandidateNumber; d++) {
            // firstly set the HDPeakIndexToPeakMatch needed for HDFragmentPairScore
            this.settings.set(VariableNames.HD_PEAK_INDEX_TO_PEAK_MATCH_NAME, peakIndexToPeakMatchHD[d]);
            for (int i = 0; i < score_types.length; i++) {
                if (this.scoreCollection.getScore(i).getValue() != null) {
                    if (this.scoreCollection.getScore(i).isUsesPiecewiseCalculation()) {
                        deuteratedCandidates[d].setProperty(score_types[i], summedScores[i] + summedScoresHD[d][i]);
                    } else if (this.scoreCollection.getScore(i).calculationFinished()) {
                        deuteratedCandidates[d].setProperty(score_types[i], this.scoreCollection.getScore(i).getValue());
                    } else if (!this.scoreCollection.getScore(i).calculationFinished()) {
                        this.scoreCollection.getScore(i).calculate();
                        deuteratedCandidates[d].setProperty(score_types[i], this.scoreCollection.getScore(i).getValue());
                    }
                }
            }
        }
        this.settings.remove(VariableNames.PEAK_INDEX_TO_PEAK_MATCH_NAME);
        this.settings.remove(VariableNames.HD_PEAK_INDEX_TO_PEAK_MATCH_NAME);
        this.candidates = deuteratedCandidates;
        for (int d = 0; d < deuteratedCandidateNumber; d++) this.candidates[d].setProperty(VariableNames.HD_GROUP_FLAG_NAME, this.candidates[0].getIdentifier());
    } catch (Exception e) {
        e.printStackTrace();
        logger.warn("candidate score calculation interrupted");
        return;
    }
    this.candidates[0].setProperty(VariableNames.HD_NUMBER_PEAKS_USED_COLUMN, tandemMassPeakListHD.getNumberPeaksUsed());
}

Example 3 with MatchPeakList

use of de.ipbhalle.metfraglib.match.MatchPeakList in project MetFragRelaunched by ipb-halle.

the class HDTopDownFragmenterAssignerScorer method matchFragment.

/**
 * checks the match of the current fragment and returns the index of the next peak
 *
 * @param tempPeakPointer
 * @param currentFragmentWrapper
 * @param tandemMassPeakList
 * @param sortedScoredPeaks
 * @param newToProcessFragments
 * @param peakIndexToPeakMatch
 * @param fragmentIndexToPeakMatch
 * @return
 */
protected boolean matchFragment(int tempPeakPointer, HDTopDownBitArrayFragmentWrapper currentFragmentWrapper, SortedTandemMassPeakList tandemMassPeakList, java.util.HashMap<Integer, MatchFragmentList> peakIndexToPeakMatch, java.util.HashMap<Integer, MatchPeakList> fragmentIndexToPeakMatch) {
    byte matched = -1;
    boolean matchedAndAdded = false;
    while (matched != 1 && tempPeakPointer >= 0) {
        IMatch[] match = new IMatch[1];
        TandemMassPeak currentPeak = tandemMassPeakList.getElement(tempPeakPointer);
        /*
			 * calculate match
			 */
        if (tempPeakPointer >= 0) {
            matched = currentFragmentWrapper.getWrappedFragment().matchToPeak(this.candidates[0].getPrecursorMolecule(), currentPeak, this.precursorIonTypeIndex, this.positiveMode, match);
        }
        /*
			 * check whether match has occurred
			 */
        if (matched == 0) {
            currentFragmentWrapper.getWrappedFragment().setPrecursorFragments(true);
            Double[][] currentScores = this.scoreCollection.calculateSingleMatch(match[0]);
            /*
				 * first generate the new fragment node and set the score values
				 */
            MatchFragmentNode newNode = new MatchFragmentNode(match[0]);
            newNode.setScore(currentScores[0][0]);
            newNode.setFragmentScores(currentScores[0]);
            newNode.setOptimalValues(currentScores[1]);
            /*
				 * find correct location in the fragment list
				 */
            boolean similarFragmentFound = false;
            if (peakIndexToPeakMatch.containsKey(tempPeakPointer)) {
                Double[] values = peakIndexToPeakMatch.get(tempPeakPointer).containsByFingerprint(currentFragmentWrapper.getWrappedFragment().getAtomsFastBitArray());
                if (values == null) {
                    peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                } else {
                    if (values[0] < currentScores[0][0]) {
                        peakIndexToPeakMatch.get(tempPeakPointer).removeElementByID((int) Math.floor(values[1]));
                        fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).removeElementByID(tempPeakPointer);
                        if (fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).getRootNode() == null) {
                            fragmentIndexToPeakMatch.remove((int) Math.floor(values[1]));
                        }
                        peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                    } else
                        similarFragmentFound = true;
                }
            } else {
                MatchFragmentList newFragmentList = new MatchFragmentList(newNode);
                peakIndexToPeakMatch.put(tempPeakPointer, newFragmentList);
            }
            /*
				 * insert peak into fragment's peak list 
				 */
            if (!similarFragmentFound) {
                if (fragmentIndexToPeakMatch.containsKey(currentFragmentWrapper.getWrappedFragment().getID())) {
                    fragmentIndexToPeakMatch.get(currentFragmentWrapper.getWrappedFragment().getID()).insert(currentPeak, currentScores[0][0], tempPeakPointer);
                } else {
                    MatchPeakList newPeakList = new MatchPeakList(currentPeak, currentScores[0][0], tempPeakPointer);
                    fragmentIndexToPeakMatch.put(currentFragmentWrapper.getWrappedFragment().getID(), newPeakList);
                }
            }
        }
        /*
			 * if the mass of the current fragment was greater than the peak mass then assign the current peak ID to the peak IDs of the
			 * child fragments as they have smaller masses 
			 */
        if (matched == 1 || tempPeakPointer == 0) {
            /*
				 * mark current fragment for further fragmentation
				 */
            currentFragmentWrapper.setCurrentPeakIndexPointer(tempPeakPointer);
        }
        /*
			 * if the current fragment has matched to the current peak then set the current peak index to the next peak as the current fragment can 
			 * also match to the next peak
			 * if the current fragment mass was smaller than that of the current peak then set the current peak index to the next peak (reduce the index) 
			 * as the next peak mass is smaller and could match the current smaller fragment mass 
			 */
        if (matched == 0 || matched == -1)
            tempPeakPointer--;
    }
    return matchedAndAdded;
}

Example 4 with MatchPeakList

use of de.ipbhalle.metfraglib.match.MatchPeakList in project MetFragRelaunched by ipb-halle.

the class TopDownFragmenterAssignerScorer method calculate.

@Override
public void calculate() {
    AbstractTopDownBitArrayPrecursor candidatePrecursor = (AbstractTopDownBitArrayPrecursor) (this.candidates[0]).getPrecursorMolecule();
    // generate root fragment to start fragmentation
    AbstractTopDownBitArrayFragment root = candidatePrecursor.toFragment();
    Byte maximumTreeDepth = (Byte) settings.get(VariableNames.MAXIMUM_TREE_DEPTH_NAME);
    if (maximumTreeDepth == 0) {
        maximumTreeDepth = candidatePrecursor.getNumNodeDegreeOne() >= 4 ? (byte) 3 : (byte) 2;
    }
    this.candidates[0].setProperty(VariableNames.MAXIMUM_TREE_DEPTH_NAME, maximumTreeDepth);
    // read peaklist
    SortedTandemMassPeakList tandemMassPeakList = (SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    tandemMassPeakList.initialiseMassLimits((Double) this.settings.get(VariableNames.RELATIVE_MASS_DEVIATION_NAME), (Double) settings.get(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME));
    Integer precursorIonType = (Integer) this.settings.get(VariableNames.PRECURSOR_ION_MODE_NAME);
    Boolean positiveMode = (Boolean) this.settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME);
    int precursorIonTypeIndex = Constants.ADDUCT_NOMINAL_MASSES.indexOf(precursorIonType);
    this.fragmenter.setMinimumFragmentMassLimit(this.fragmenter.getMinimumFragmentMassLimit() - Constants.ADDUCT_MASSES.get(precursorIonTypeIndex));
    /*
		 * prepare the processing
		 */
    java.util.Queue<AbstractTopDownBitArrayFragmentWrapper> toProcessFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragmentWrapper>();
    /*
		 * wrap the root fragment
		 */
    AbstractTopDownBitArrayFragmentWrapper rootFragmentWrapper = new AbstractTopDownBitArrayFragmentWrapper(root, tandemMassPeakList.getNumberElements() - 1);
    toProcessFragments.add(rootFragmentWrapper);
    java.util.HashMap<Integer, MatchFragmentList> peakIndexToPeakMatch = new java.util.HashMap<Integer, MatchFragmentList>();
    java.util.HashMap<Integer, MatchPeakList> fragmentIndexToPeakMatch = new java.util.HashMap<Integer, MatchPeakList>();
    /*
		 * iterate over the maximal allowed tree depth
		 */
    for (int k = 1; k <= maximumTreeDepth; k++) {
        java.util.Queue<AbstractTopDownBitArrayFragmentWrapper> newToProcessFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragmentWrapper>();
        /*
			 * use each fragment that is marked as to be processed
			 */
        while (!toProcessFragments.isEmpty()) {
            /*
				 * generate fragments of new tree depth
				 */
            AbstractTopDownBitArrayFragmentWrapper wrappedPrecursorFragment = toProcessFragments.poll();
            if (wrappedPrecursorFragment.getWrappedFragment().isDiscardedForFragmentation()) {
                AbstractTopDownBitArrayFragment clonedFragment = (AbstractTopDownBitArrayFragment) wrappedPrecursorFragment.getWrappedFragment().clone(candidatePrecursor);
                clonedFragment.setAsDiscardedForFragmentation();
                if (clonedFragment.getTreeDepth() < maximumTreeDepth)
                    newToProcessFragments.add(new AbstractTopDownBitArrayFragmentWrapper(clonedFragment, wrappedPrecursorFragment.getCurrentPeakIndexPointer()));
                continue;
            }
            /*
				 * generate fragments of next tree depth
				 */
            java.util.ArrayList<AbstractTopDownBitArrayFragment> fragmentsOfCurrentTreeDepth = this.fragmenter.getFragmentsOfNextTreeDepth(wrappedPrecursorFragment.getWrappedFragment());
            /*
				 * get peak pointer of current precursor fragment
				 */
            int currentPeakPointer = wrappedPrecursorFragment.getCurrentPeakIndexPointer();
            /*
				 * start loop over all child fragments from precursor fragment
				 * to try assigning them to the current peak
				 */
            for (int l = 0; l < fragmentsOfCurrentTreeDepth.size(); l++) {
                AbstractTopDownBitArrayFragment currentFragment = fragmentsOfCurrentTreeDepth.get(l);
                if (!fragmentsOfCurrentTreeDepth.get(l).isValidFragment()) {
                    if (currentFragment.getTreeDepth() < maximumTreeDepth)
                        newToProcessFragments.add(new AbstractTopDownBitArrayFragmentWrapper(fragmentsOfCurrentTreeDepth.get(l), currentPeakPointer));
                    continue;
                }
                if (this.wasAlreadyGeneratedByHashtable(currentFragment)) {
                    currentFragment.setAsDiscardedForFragmentation();
                    if (currentFragment.getTreeDepth() < maximumTreeDepth)
                        newToProcessFragments.add(new AbstractTopDownBitArrayFragmentWrapper(currentFragment, currentPeakPointer));
                    continue;
                }
                byte matched = -1;
                int tempPeakPointer = currentPeakPointer;
                while (matched != 1 && tempPeakPointer >= 0) {
                    IMatch[] match = new IMatch[1];
                    /*
						 * calculate match
						 */
                    matched = currentFragment.matchToPeak(candidatePrecursor, tandemMassPeakList.getElement(tempPeakPointer), precursorIonTypeIndex, positiveMode, match);
                    /*
						 * check whether match has occurred
						 */
                    if (matched == 0) {
                        currentFragment.setPrecursorFragments(true);
                        Double[][] currentScores = this.scoreCollection.calculateSingleMatch(match[0]);
                        /*
							 * insert fragment into peak's fragment list 
							 */
                        /*
							 * first generate the new fragment node and set the score values
							 */
                        MatchFragmentNode newNode = new MatchFragmentNode(match[0]);
                        newNode.setScore(currentScores[0][0]);
                        newNode.setFragmentScores(currentScores[0]);
                        newNode.setOptimalValues(currentScores[1]);
                        /*
							 * find correct location in the fragment list
							 */
                        boolean similarFragmentFound = false;
                        if (peakIndexToPeakMatch.containsKey(tempPeakPointer)) {
                            Double[] values = peakIndexToPeakMatch.get(tempPeakPointer).containsByFingerprint(currentFragment.getAtomsFastBitArray());
                            if (values == null) {
                                peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                            } else {
                                if (values[0] < currentScores[0][0]) {
                                    peakIndexToPeakMatch.get(tempPeakPointer).removeElementByID((int) Math.floor(values[1]));
                                    fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).removeElementByID(tempPeakPointer);
                                    if (fragmentIndexToPeakMatch.get((int) Math.floor(values[1])).getRootNode() == null) {
                                        fragmentIndexToPeakMatch.remove((int) Math.floor(values[1]));
                                    }
                                    peakIndexToPeakMatch.get(tempPeakPointer).insert(newNode);
                                } else
                                    similarFragmentFound = true;
                            }
                        } else {
                            MatchFragmentList newFragmentList = new MatchFragmentList(newNode);
                            peakIndexToPeakMatch.put(tempPeakPointer, newFragmentList);
                        }
                        /*
							 * insert peak into fragment's peak list 
							 */
                        if (!similarFragmentFound) {
                            if (fragmentIndexToPeakMatch.containsKey(currentFragment.getID())) {
                                fragmentIndexToPeakMatch.get(currentFragment.getID()).insert(tandemMassPeakList.getElement(tempPeakPointer), currentScores[0][0], tempPeakPointer);
                            } else {
                                MatchPeakList newPeakList = new MatchPeakList(tandemMassPeakList.getElement(tempPeakPointer), currentScores[0][0], tempPeakPointer);
                                fragmentIndexToPeakMatch.put(currentFragment.getID(), newPeakList);
                            }
                        }
                    }
                    /*
						 * if the mass of the current fragment was greater than the peak mass then assign the current peak ID to the peak IDs of the
						 * child fragments as they have smaller masses 
						 */
                    if (matched == 1 || tempPeakPointer == 0) {
                        /*
							 * mark current fragment for further fragmentation
							 */
                        if (currentFragment.getTreeDepth() < maximumTreeDepth)
                            newToProcessFragments.add(new AbstractTopDownBitArrayFragmentWrapper(currentFragment, tempPeakPointer));
                    }
                    /*
						 * if the current fragment has matched to the current peak then set the current peak index to the next peak as the current fragment can 
						 * also match to the next peak
						 * if the current fragment mass was smaller than that of the current peak then set the current peak index to the next peak (reduce the index) 
						 * as the next peak mass is smaller and could match the current smaller fragment mass 
						 */
                    if (matched == 0 || matched == -1)
                        tempPeakPointer--;
                }
            }
        }
        toProcessFragments = newToProcessFragments;
    }
    toProcessFragments.clear();
    this.matchList = new MatchList();
    /*
		 * collect score of all scores over all matches
		 */
    double[][] singleScores = new double[this.scoreCollection.getNumberScores()][peakIndexToPeakMatch.size()];
    /*
		 * collect the sum of all scores over all matches
		 */
    double[] summedScores = new double[this.scoreCollection.getNumberScores()];
    java.util.Iterator<Integer> it = peakIndexToPeakMatch.keySet().iterator();
    int index = 0;
    /*
		 * go over peak matches
		 */
    while (it.hasNext()) {
        int key = it.next();
        MatchFragmentList matchFragmentList = peakIndexToPeakMatch.get(key);
        MatchFragmentNode bestFragment = matchFragmentList.getRootNode();
        IMatch match = bestFragment.getMatch();
        Double[] scoreValuesSingleMatch = null;
        try {
            scoreValuesSingleMatch = bestFragment.getFragmentScores();
        } catch (Exception e) {
            matchFragmentList.printElements(this.candidates[0].getPrecursorMolecule());
            System.out.println(this.candidates[0].getIdentifier() + " " + key);
            System.exit(1);
        }
        Double[] optimalValuesSingleMatch = bestFragment.getOptimalValues();
        for (int k = 1; k < scoreValuesSingleMatch.length; k++) {
            if (optimalValuesSingleMatch[k] != null)
                singleScores[k - 1][index] = optimalValuesSingleMatch[k];
            summedScores[k - 1] += scoreValuesSingleMatch[k];
        }
        if (bestFragment != null) {
            bestFragment.getFragment().setIsBestMatchedFragment(true);
            // match.initialiseBestMatchedFragmentByFragmentID(bestFragment.getFragment().getID());
            this.matchList.addElementSorted(match);
            MatchFragmentNode currentFragment = bestFragment;
            while (currentFragment.hasNext()) {
                MatchFragmentNode node = currentFragment.getNext();
                match.addToMatch(node.getMatch());
                currentFragment = currentFragment.getNext();
            }
        }
        index++;
    }
    for (int i = 0; i < this.matchList.getNumberElements(); i++) this.matchList.getElement(i).shallowNullify();
    this.settings.set(VariableNames.MATCH_LIST_NAME, this.matchList);
    this.candidates[0].setMatchList(this.matchList);
    if (this.scoreCollection == null)
        return;
    try {
        for (int i = 0; i < this.scoreCollection.getNumberScores(); i++) {
            if (!this.scoreCollection.getScore(i).calculationFinished()) {
                this.scoreCollection.getScore(i).calculate();
            } else
                this.scoreCollection.getScore(i).setValue(summedScores[i]);
            if (singleScores[i].length != 0 && this.scoreCollection.getScore(i).hasInterimResults() && !this.scoreCollection.getScore(i).isInterimResultsCalculated()) {
                this.scoreCollection.getScore(i).setOptimalValues(singleScores[i]);
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        logger.warn("candidate score calculation interrupted");
        return;
    }
}