Examples with AbstractTopDownBitArrayPrecursor de.ipbhalle.metfraglib.precursor.AbstractTopDownBitArrayPrecursor used on opensource projects

Example 1 with AbstractTopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.AbstractTopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class TopDownNeutralLossFragmenter method generateFragments.

public FragmentList generateFragments() {
    FragmentList generatedFragments = new FragmentList();
    java.util.Queue<AbstractTopDownBitArrayFragment> temporaryFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragment>();
    java.util.Queue<Byte> numberOfFragmentAddedToQueue = new java.util.LinkedList<Byte>();
    java.util.Queue<de.ipbhalle.metfraglib.FastBitArray> nextBondIndecesToRemove = new java.util.LinkedList<de.ipbhalle.metfraglib.FastBitArray>();
    /*
		 * set first fragment as root for fragment generation (precursor)
		 */
    AbstractTopDownBitArrayFragment root = ((AbstractTopDownBitArrayPrecursor) this.scoredCandidate.getPrecursorMolecule()).toFragment();
    root.setID(++this.numberOfGeneratedFragments);
    root.setWasRingCleavedFragment(false);
    generatedFragments.addElement(root);
    temporaryFragments.add(root);
    numberOfFragmentAddedToQueue.add((byte) 1);
    nextBondIndecesToRemove.add(root.getBondsFastBitArray());
    for (int k = 1; k <= this.maximumTreeDepth; k++) {
        java.util.Queue<AbstractTopDownBitArrayFragment> newTemporaryFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragment>();
        java.util.Queue<Byte> newNumberOfFragmentAddedToQueue = new java.util.LinkedList<Byte>();
        java.util.Queue<de.ipbhalle.metfraglib.FastBitArray> newNextBondIndecesToRemove = new java.util.LinkedList<de.ipbhalle.metfraglib.FastBitArray>();
        while (!temporaryFragments.isEmpty()) {
            AbstractTopDownBitArrayFragment nextTopDownFragmentForFragmentation = temporaryFragments.poll();
            byte numberOfNextTopDownFragmentForFragmentationAddedToQueue = numberOfFragmentAddedToQueue.poll();
            int[] indecesOfSetBondsOfNextTopDownFragment = nextBondIndecesToRemove.poll().getSetIndeces();
            for (int i = 0; i < indecesOfSetBondsOfNextTopDownFragment.length; i++) {
                short nextBondIndexToRemove = (short) indecesOfSetBondsOfNextTopDownFragment[i];
                /*
					 * if index of selected bond is smaller than the maximum
					 * index of a cleaved bond of the fragment then select
					 * another bond prevents generating fragments redundantly
					 */
                if (nextBondIndexToRemove < nextTopDownFragmentForFragmentation.getMaximalIndexOfRemovedBond() || !nextTopDownFragmentForFragmentation.getBondsFastBitArray().get(nextBondIndexToRemove)) {
                    continue;
                }
                short[] indecesOfBondConnectedAtoms = ((AbstractTopDownBitArrayPrecursor) this.scoredCandidate.getPrecursorMolecule()).getConnectedAtomIndecesOfBondIndex(nextBondIndexToRemove);
                /*
					 * getting fragment generated by cleavage of the current
					 * bond "nextBondIndexToRemove"
					 */
                AbstractTopDownBitArrayFragment[] newGeneratedTopDownFragments = nextTopDownFragmentForFragmentation.traverseMolecule(this.scoredCandidate.getPrecursorMolecule(), nextBondIndexToRemove, indecesOfBondConnectedAtoms);
                /*
					 * if we got two fragments then save these as valid ones
					 */
                if (newGeneratedTopDownFragments.length == 2) {
                    this.checkForNeutralLossesAdaptMolecularFormulas(newGeneratedTopDownFragments, nextBondIndexToRemove);
                    if (newGeneratedTopDownFragments[0].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        newGeneratedTopDownFragments[0].setID(++this.numberOfGeneratedFragments);
                        generatedFragments.addElement(newGeneratedTopDownFragments[0]);
                        newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        newNumberOfFragmentAddedToQueue.add((byte) 1);
                        newTemporaryFragments.add(newGeneratedTopDownFragments[0]);
                    }
                    if (newGeneratedTopDownFragments[1].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        newGeneratedTopDownFragments[1].setID(++this.numberOfGeneratedFragments);
                        generatedFragments.addElement(newGeneratedTopDownFragments[1]);
                        newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[1].getBondsFastBitArray());
                        newNumberOfFragmentAddedToQueue.add((byte) 1);
                        newTemporaryFragments.add(newGeneratedTopDownFragments[1]);
                    }
                } else /*
					 * if just one fragment then we have to cleave once again
					 */
                {
                    if (newGeneratedTopDownFragments[0].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        if (numberOfNextTopDownFragmentForFragmentationAddedToQueue < this.maximumNumberOfAFragmentAddedToQueue) {
                            temporaryFragments.add(newGeneratedTopDownFragments[0]);
                            numberOfFragmentAddedToQueue.add((byte) (numberOfNextTopDownFragmentForFragmentationAddedToQueue + 1));
                            // nextBondIndecesToRemove.add(this.precursorMolecule.getFastBitArrayOfBondsBelongingtoRingLikeBondIndex(nextBondIndexToRemove));
                            nextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        } else {
                            newTemporaryFragments.add(newGeneratedTopDownFragments[0]);
                            newNumberOfFragmentAddedToQueue.add((byte) 1);
                            newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        }
                    }
                }
            }
        }
        temporaryFragments = newTemporaryFragments;
        numberOfFragmentAddedToQueue = newNumberOfFragmentAddedToQueue;
        nextBondIndecesToRemove = newNextBondIndecesToRemove;
    }
    temporaryFragments = null;
    numberOfFragmentAddedToQueue = null;
    nextBondIndecesToRemove = null;
    return generatedFragments;
}

Example 2 with AbstractTopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.AbstractTopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class PFAS method getSplitResult.

public FragmentPFAS getSplitResult(List<Integer> bondIndexes, int[] endChainCarbonIndexes) {
    LinkedList<AbstractTopDownBitArrayFragment> abstractTopDownBitArrayFragments = new LinkedList<AbstractTopDownBitArrayFragment>();
    LinkedList<AbstractTopDownBitArrayFragment> newAbstractTopDownBitArrayFragments = null;
    AbstractTopDownBitArrayFragment root = ((AbstractTopDownBitArrayPrecursor) this.pfasStructure.getPrecursorMolecule()).toFragment();
    abstractTopDownBitArrayFragments.add(root);
    int bondsBroken = 0;
    List<AbstractTopDownBitArrayFragment> createdFragments = new ArrayList<AbstractTopDownBitArrayFragment>();
    // store atoms
    List<short[]> indecesOfBondConnectedAtomsList = new ArrayList<short[]>();
    for (int i = 0; i < bondIndexes.size(); i++) {
        int bondIndex = bondIndexes.get(i);
        newAbstractTopDownBitArrayFragments = new LinkedList<AbstractTopDownBitArrayFragment>();
        while (!abstractTopDownBitArrayFragments.isEmpty()) {
            AbstractTopDownBitArrayFragment currentFragment = abstractTopDownBitArrayFragments.remove();
            if (currentFragment.getBondsFastBitArray().get(bondIndex)) {
                short[] indecesOfBondConnectedAtoms = new short[2];
                AbstractTopDownBitArrayFragment[] fragments = this.split((short) bondIndex, currentFragment, indecesOfBondConnectedAtoms);
                if (fragments.length != 1)
                    bondsBroken++;
                for (int ii = 0; ii < fragments.length; ii++) {
                    newAbstractTopDownBitArrayFragments.add(fragments[ii]);
                    createdFragments.add(fragments[ii]);
                    indecesOfBondConnectedAtomsList.add(indecesOfBondConnectedAtoms);
                }
            }
        }
        abstractTopDownBitArrayFragments = newAbstractTopDownBitArrayFragments;
    }
    List<short[]> cleanedIndecesOfBondConnectedAtomsList = new ArrayList<short[]>();
    List<AbstractTopDownBitArrayFragment> cleanedCreatedFragments = new ArrayList<AbstractTopDownBitArrayFragment>();
    for (int i = 0; i < createdFragments.size(); i++) {
        boolean bondFound = false;
        for (int j = 0; j < bondIndexes.size(); j++) {
            if (createdFragments.get(i).getBondsFastBitArray().get(bondIndexes.get(j))) {
                bondFound = true;
            }
        }
        if (!bondFound) {
            cleanedCreatedFragments.add(createdFragments.get(i));
            cleanedIndecesOfBondConnectedAtomsList.add(indecesOfBondConnectedAtomsList.get(i));
        }
    }
    boolean[] containsEndChainCarbon = new boolean[cleanedCreatedFragments.size()];
    for (int i = 0; i < cleanedCreatedFragments.size(); i++) {
        for (int ii = 0; ii < endChainCarbonIndexes.length; ii++) {
            if (cleanedCreatedFragments.get(i).getAtomsFastBitArray().get(endChainCarbonIndexes[ii]))
                containsEndChainCarbon[i] = true;
        }
    }
    int fragmentsWithEndChainCarbonCount = 0;
    for (boolean fragmentsWithEndChainCarbon : containsEndChainCarbon) if (fragmentsWithEndChainCarbon)
        fragmentsWithEndChainCarbonCount++;
    if (fragmentsWithEndChainCarbonCount == 0) {
        System.err.println("Error: Problem occured. Check input molecule. No PFAS left after split.");
        return null;
    }
    for (int i = 0; i < containsEndChainCarbon.length; i++) if (!containsEndChainCarbon[i])
        return new FragmentPFAS(cleanedCreatedFragments, cleanedIndecesOfBondConnectedAtomsList, containsEndChainCarbon, bondsBroken, this.pfasStructure);
    return null;
}

Example 3 with AbstractTopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.AbstractTopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class TopDownFragmenter method generateFragments.

public FragmentList generateFragments() {
    FragmentList generatedFragments = new FragmentList();
    java.util.Queue<AbstractTopDownBitArrayFragment> temporaryFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragment>();
    java.util.Queue<Byte> numberOfFragmentAddedToQueue = new java.util.LinkedList<Byte>();
    java.util.Queue<de.ipbhalle.metfraglib.FastBitArray> nextBondIndecesToRemove = new java.util.LinkedList<de.ipbhalle.metfraglib.FastBitArray>();
    /*
		 * set first fragment as root for fragment generation (precursor)
		 */
    AbstractTopDownBitArrayFragment root = ((AbstractTopDownBitArrayPrecursor) this.scoredCandidate.getPrecursorMolecule()).toFragment();
    root.setID(++this.numberOfGeneratedFragments);
    temporaryFragments.add(root);
    generatedFragments.addElement(root);
    numberOfFragmentAddedToQueue.add((byte) 1);
    nextBondIndecesToRemove.add(root.getBondsFastBitArray());
    for (int k = 1; k <= this.maximumTreeDepth; k++) {
        java.util.Queue<AbstractTopDownBitArrayFragment> newTemporaryFragments = new java.util.LinkedList<AbstractTopDownBitArrayFragment>();
        java.util.Queue<Byte> newNumberOfFragmentAddedToQueue = new java.util.LinkedList<Byte>();
        java.util.Queue<de.ipbhalle.metfraglib.FastBitArray> newNextBondIndecesToRemove = new java.util.LinkedList<de.ipbhalle.metfraglib.FastBitArray>();
        while (!temporaryFragments.isEmpty()) {
            AbstractTopDownBitArrayFragment nextTopDownFragmentForFragmentation = temporaryFragments.poll();
            byte numberOfNextTopDownFragmentForFragmentationAddedToQueue = numberOfFragmentAddedToQueue.poll();
            int[] indecesOfSetBondsOfNextTopDownFragment = nextBondIndecesToRemove.poll().getSetIndeces();
            for (int i = 0; i < indecesOfSetBondsOfNextTopDownFragment.length; i++) {
                short nextBondIndexToRemove = (short) indecesOfSetBondsOfNextTopDownFragment[i];
                /*
					* if index of selected bond is smaller than the maximum index of a cleaved bond of the
					* fragment then select another bond
					* prevents generating fragments redundantly
					*/
                if (nextBondIndexToRemove < nextTopDownFragmentForFragmentation.getMaximalIndexOfRemovedBond() || !nextTopDownFragmentForFragmentation.getBondsFastBitArray().get(nextBondIndexToRemove)) {
                    continue;
                }
                short[] indecesOfBondConnectedAtoms = ((BitArrayPrecursor) this.scoredCandidate.getPrecursorMolecule()).getConnectedAtomIndecesOfBondIndex(nextBondIndexToRemove);
                /*
					* getting fragment generated by cleavage of the current bond "nextBondIndexToRemove"
					*/
                AbstractTopDownBitArrayFragment[] newGeneratedTopDownFragments = nextTopDownFragmentForFragmentation.traverseMolecule(this.scoredCandidate.getPrecursorMolecule(), nextBondIndexToRemove, indecesOfBondConnectedAtoms);
                /* 
					 * if we got two fragments then save these as valid ones
					 */
                if (newGeneratedTopDownFragments.length == 2) {
                    if (newGeneratedTopDownFragments[0].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        newGeneratedTopDownFragments[0].setID(++this.numberOfGeneratedFragments);
                        generatedFragments.addElement(newGeneratedTopDownFragments[0]);
                        newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        newNumberOfFragmentAddedToQueue.add((byte) 1);
                        newTemporaryFragments.add(newGeneratedTopDownFragments[0]);
                    }
                    if (newGeneratedTopDownFragments[1].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        newGeneratedTopDownFragments[1].setID(++this.numberOfGeneratedFragments);
                        generatedFragments.addElement(newGeneratedTopDownFragments[1]);
                        newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[1].getBondsFastBitArray());
                        newNumberOfFragmentAddedToQueue.add((byte) 1);
                        newTemporaryFragments.add(newGeneratedTopDownFragments[1]);
                    }
                } else /*
					 *  if just one fragment then we have to cleave once again
					 */
                {
                    if (newGeneratedTopDownFragments[0].getMonoisotopicMass(this.scoredCandidate.getPrecursorMolecule()) > this.minimumFragmentMassLimit - this.minimumMassDeviationForFragmentGeneration) {
                        if (numberOfNextTopDownFragmentForFragmentationAddedToQueue < this.maximumNumberOfAFragmentAddedToQueue) {
                            temporaryFragments.add(newGeneratedTopDownFragments[0]);
                            numberOfFragmentAddedToQueue.add((byte) (numberOfNextTopDownFragmentForFragmentationAddedToQueue + 1));
                            // nextBondIndecesToRemove.add(this.precursorMolecule.getFastBitArrayOfBondsBelongingtoRingLikeBondIndex(nextBondIndexToRemove));
                            nextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        } else {
                            newTemporaryFragments.add(newGeneratedTopDownFragments[0]);
                            newNumberOfFragmentAddedToQueue.add((byte) 1);
                            newNextBondIndecesToRemove.add(newGeneratedTopDownFragments[0].getBondsFastBitArray());
                        }
                    }
                }
            }
        }
        temporaryFragments = newTemporaryFragments;
        numberOfFragmentAddedToQueue = newNumberOfFragmentAddedToQueue;
        nextBondIndecesToRemove = newNextBondIndecesToRemove;
    }
    temporaryFragments = null;
    numberOfFragmentAddedToQueue = null;
    nextBondIndecesToRemove = null;
    return generatedFragments;
}

Example 4 with AbstractTopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.AbstractTopDownBitArrayPrecursor 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;
    }
}