Examples with FingerprintGroup de.ipbhalle.metfraglib.substructure.FingerprintGroup used on opensource projects

Example 1 with FingerprintGroup

use of de.ipbhalle.metfraglib.substructure.FingerprintGroup in project MetFragRelaunched by ipb-halle.

the class AutomatedLossFingerprintAnnotationScoreInitialiser method initScoreParameters.

@Override
public void initScoreParameters(Settings settings) throws Exception {
    if (!settings.containsKey(VariableNames.LOSS_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME) || settings.get(VariableNames.LOSS_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME) == null) {
        MassToFingerprintGroupListCollection lossToFingerprintGroupListCollection = new MassToFingerprintGroupListCollection();
        DefaultPeakList peakList = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
        Double mzppm = (Double) settings.get(VariableNames.RELATIVE_MASS_DEVIATION_NAME);
        Double mzabs = (Double) settings.get(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME);
        BufferedReader breader = null;
        java.io.InputStream is = null;
        if (settings.containsKey(VariableNames.FINGERPRINT_LOSS_ANNOTATION_FILE_NAME) && settings.get(VariableNames.FINGERPRINT_LOSS_ANNOTATION_FILE_NAME) != null) {
            breader = new BufferedReader(new FileReader(new File((String) settings.get(VariableNames.FINGERPRINT_LOSS_ANNOTATION_FILE_NAME))));
        } else {
            String filename = "loss_annotations_neg.txt";
            if ((Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME))
                filename = "loss_annotations_pos.txt";
            is = AutomatedPeakFingerprintAnnotationScoreInitialiser.class.getResourceAsStream("/" + filename);
            breader = new java.io.BufferedReader(new java.io.InputStreamReader(is));
        }
        Double neutralPrecursorMass = (Double) settings.get(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME);
        Double adductMass = Constants.getIonisationTypeMassCorrection(Constants.ADDUCT_NOMINAL_MASSES.indexOf((Integer) settings.get(VariableNames.PRECURSOR_ION_MODE_NAME)), (Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME));
        java.util.ArrayList<Double> massDifferences = this.calculatePeakDifferences(peakList, neutralPrecursorMass, adductMass);
        java.util.ArrayList<Double> uniqueMassDifferences = this.calculateUniquePeakDifferences(massDifferences, mzppm, mzabs);
        java.util.LinkedList<Double> lossMassesFound = new java.util.LinkedList<Double>();
        String line = "";
        int numMatchedObservationsMerged = 0;
        java.util.HashMap<Double, MassToFingerprintGroupList> mergedFingerprintGroupLists = new java.util.HashMap<Double, MassToFingerprintGroupList>();
        this.setPseudoCountValues(settings);
        // first add non-matched masses with dummy fingerprint "0"
        // these masses are present in the first line of the annotation file: mass[:counts]
        String nonMatchedMassesString = breader.readLine().trim();
        int numNonMatchElements = 0;
        int numNonMatchOccurrences = 0;
        if (!nonMatchedMassesString.equals("NA")) {
            // masses are separated by ";"
            String[] tmp = nonMatchedMassesString.split(";");
            numNonMatchElements = tmp.length;
            for (int k = 0; k < tmp.length; k++) {
                // run over all masses
                // split by ":" to separate mass[:counts]
                String[] tmp2 = tmp[k].split("\\s+");
                int count = 1;
                // create mass value
                Double newMass = Double.parseDouble(tmp2[0]);
                // if count is present use count else use 1 (default)
                if (tmp2.length == 2)
                    count = Integer.parseInt(tmp2[1]);
                // save number non-matched occurences
                numNonMatchOccurrences += count;
                // check whether the newMass is also present in our found peak list losses
                Double matchedMass = this.containsMass(newMass, uniqueMassDifferences, mzabs, mzppm);
                // if not present and already larger than largest peak mass stop here
                if (matchedMass == null && newMass > peakList.getMaximumMassValue())
                    break;
                if (matchedMass != null) {
                    // if loss is present in our peak list add it to the annotation list
                    // prepare new element
                    FingerprintGroup group = new FingerprintGroup(1.0);
                    group.setNumberObserved(count);
                    group.setFingerprint("0");
                    if (mergedFingerprintGroupLists.containsKey(matchedMass)) {
                        // check if the mass was already inserted
                        MassToFingerprintGroupList currentGroupList = mergedFingerprintGroupLists.get(matchedMass);
                        FingerprintGroup curGroup = currentGroupList.getElementByFingerprint(group.getFingerprint());
                        // check if fingerprint was already inserted
                        if (// if not simply add it
                        curGroup == null)
                            // if not simply add it
                            currentGroupList.addElement(group);
                        else {
                            // if already present decrease number observed elements (as already observed)
                            numNonMatchElements--;
                            // adapt values
                            curGroup.setNumberObserved(curGroup.getNumberObserved() + group.getNumberObserved());
                            curGroup.setProbability(curGroup.getProbability() + group.getProbability());
                        }
                    } else {
                        // if mass not yet present simply add it
                        MassToFingerprintGroupList currentGroupList = new MassToFingerprintGroupList(matchedMass);
                        currentGroupList.addElement(group);
                        mergedFingerprintGroupLists.put(matchedMass, currentGroupList);
                    }
                }
            }
        }
        // now add loss-fingerprint assignments which were annotated in the training
        while ((line = breader.readLine()) != null) {
            line = line.trim();
            if (line.length() == 0)
                continue;
            if (line.startsWith("#"))
                continue;
            if (line.startsWith("SUMMARY")) {
                String[] tmp = line.split("\\s+");
                // sum overall occurrences
                settings.set(VariableNames.LOSS_FINGERPRINT_DENOMINATOR_COUNT_NAME, Double.parseDouble(tmp[2]) + numNonMatchOccurrences);
                // number different peak pairs matched
                settings.set(VariableNames.LOSS_FINGERPRINT_MATCHED_TUPLE_COUNT_NAME, Double.parseDouble(tmp[1]) - numMatchedObservationsMerged);
                // number different peak pairs non-matched
                settings.set(VariableNames.LOSS_FINGERPRINT_NON_MATCHED_TUPLE_COUNT_NAME, (double) numNonMatchElements);
                continue;
            }
            String[] tmp = line.split("\\s+");
            Double loss = Double.parseDouble(tmp[0]);
            // check whether the current loss in our annotation is also present in the peak list
            Double matchedMass = this.containsMass(loss, uniqueMassDifferences, mzabs, mzppm);
            if (matchedMass != null) {
                // if yes we need to consider it
                // create fingerprint groups from annotation entry
                FingerprintGroup[] groups = this.getFingerprintGroup(tmp);
                if (mergedFingerprintGroupLists.containsKey(matchedMass)) {
                    // check whether mass is already present
                    MassToFingerprintGroupList currentGroupList = mergedFingerprintGroupLists.get(matchedMass);
                    for (int i = 0; i < groups.length; i++) {
                        // check if fingerprint is already inserted
                        FingerprintGroup curGroup = currentGroupList.getElementByFingerprint(groups[i].getFingerprint());
                        if (// if not simply add it
                        curGroup == null)
                            // if not simply add it
                            currentGroupList.addElement(groups[i]);
                        else {
                            // otherwise increase the number of matched observations to adapt number of unique tupels
                            if (curGroup.getFingerprint().getSize() != 1)
                                numMatchedObservationsMerged++;
                            // adapt loss-fingerprint assignment values
                            curGroup.setNumberObserved(curGroup.getNumberObserved() + groups[i].getNumberObserved());
                            curGroup.setProbability(curGroup.getProbability() + groups[i].getProbability());
                        }
                    }
                } else {
                    // if mass not yet present simply add it
                    MassToFingerprintGroupList currentGroupList = new MassToFingerprintGroupList(matchedMass);
                    for (int i = 0; i < groups.length; i++) currentGroupList.addElement(groups[i]);
                    mergedFingerprintGroupLists.put(matchedMass, currentGroupList);
                }
            }
        }
        java.util.Iterator<Double> it = mergedFingerprintGroupLists.keySet().iterator();
        while (it.hasNext()) {
            lossToFingerprintGroupListCollection.addElementSorted(mergedFingerprintGroupLists.get(it.next()));
        }
        // store all mass differences (losses) found in the peak list
        for (int i = 0; i < massDifferences.size(); i++) {
            if (lossToFingerprintGroupListCollection.getElementByPeak(massDifferences.get(i), mzppm, mzabs) != null)
                lossMassesFound.add(massDifferences.get(i));
        }
        breader.close();
        settings.set(VariableNames.LOSS_MASSES_FOUND_PEAKLIST_NAME, lossMassesFound);
        settings.set(VariableNames.LOSS_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME, lossToFingerprintGroupListCollection);
    }
}

Example 2 with FingerprintGroup

use of de.ipbhalle.metfraglib.substructure.FingerprintGroup in project MetFragRelaunched by ipb-halle.

the class AutomatedLossFingerprintAnnotationScoreInitialiser method getFingerprintGroup.

protected FingerprintGroup[] getFingerprintGroup(String[] splittedLine) {
    FingerprintGroup[] groups = new FingerprintGroup[(splittedLine.length - 1) / 2];
    int index = 0;
    for (int i = 1; i < splittedLine.length; i += 2) {
        double count = Double.parseDouble(splittedLine[i]);
        FingerprintGroup newGroup = new FingerprintGroup(count);
        newGroup.setNumberObserved((int) count);
        newGroup.setFingerprint(splittedLine[i + 1]);
        groups[index] = newGroup;
        index++;
    }
    return groups;
}

Example 3 with FingerprintGroup

use of de.ipbhalle.metfraglib.substructure.FingerprintGroup in project MetFragRelaunched by ipb-halle.

the class AutomatedPeakFingerprintAnnotationScore method singlePostCalculate.

@Override
public void singlePostCalculate() {
    this.value = 0.0;
    MassToFingerprintGroupListCollection peakToFingerprintGroupListCollection = (MassToFingerprintGroupListCollection) this.settings.get(VariableNames.PEAK_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME);
    java.util.ArrayList<?> peakMatchList = (java.util.ArrayList<?>) this.candidate.getProperty("PeakMatchList");
    int matches = 0;
    // get foreground fingerprint observations (m_f_observed)
    java.util.ArrayList<Double> matchMasses = new java.util.ArrayList<Double>();
    java.util.ArrayList<Double> matchProb = new java.util.ArrayList<Double>();
    // found - 1; non-found - 2 (fp="0"); alpha - 3; beta - 4
    java.util.ArrayList<Integer> matchType = new java.util.ArrayList<Integer>();
    // get foreground fingerprint observations (m_f_observed)
    for (int i = 0; i < peakToFingerprintGroupListCollection.getNumberElements(); i++) {
        // get f_m_observed
        MassToFingerprintGroupList peakToFingerprintGroupList = peakToFingerprintGroupListCollection.getElement(i);
        Double currentMass = peakToFingerprintGroupList.getPeakmz();
        MassFingerprintMatch currentMatch = getMatchByMass(peakMatchList, currentMass);
        if (currentMatch == null) {
            FingerprintGroup fg = peakToFingerprintGroupList.getElementByFingerprint(new FastBitArray("0"));
            if (fg == null) {
                matchProb.add(peakToFingerprintGroupList.getBetaProb());
                matchType.add(4);
                this.value += Math.log(peakToFingerprintGroupList.getBetaProb());
            } else {
                matchProb.add(fg.getProbability());
                matchType.add(2);
                this.value += Math.log(fg.getProbability());
            }
            matchMasses.add(currentMass);
        } else {
            FastBitArray currentFingerprint = new FastBitArray(currentMatch.getFingerprint());
            // ToDo: at this stage try to check all fragments not only the best one
            // (p(m,f) + alpha) / sum_F(p(m,f)) + |F| * alpha
            double matching_prob = peakToFingerprintGroupList.getMatchingProbability(currentFingerprint);
            // |F|
            if (matching_prob != 0.0) {
                this.value += Math.log(matching_prob);
                matchProb.add(matching_prob);
                matchMasses.add(currentMass);
                if (currentFingerprint.getSize() != 1) {
                    matches++;
                    matchType.add(1);
                } else
                    matchType.add(2);
            } else {
                if (currentFingerprint.equals(new FastBitArray("0")) && peakToFingerprintGroupList.getElementByFingerprint(currentFingerprint) == null) {
                    matchType.add(4);
                    matchProb.add(peakToFingerprintGroupList.getBetaProb());
                    this.value += Math.log(peakToFingerprintGroupList.getBetaProb());
                } else {
                    this.value += Math.log(peakToFingerprintGroupList.getAlphaProb());
                    matchProb.add(peakToFingerprintGroupList.getAlphaProb());
                    matchType.add(3);
                }
                matchMasses.add(currentMass);
            }
        }
    }
    if (peakToFingerprintGroupListCollection.getNumberElements() == 0)
        this.value = 0.0;
    this.candidate.setProperty("AutomatedPeakFingerprintAnnotationScore_Matches", matches);
    this.candidate.setProperty("AutomatedPeakFingerprintAnnotationScore", this.value);
    this.candidate.setProperty("AutomatedPeakFingerprintAnnotationScore_Probtypes", this.getProbTypeString(matchProb, matchType, matchMasses));
    this.candidate.removeProperty("PeakMatchList");
}

Example 4 with FingerprintGroup

use of de.ipbhalle.metfraglib.substructure.FingerprintGroup in project MetFragRelaunched by ipb-halle.

the class AutomatedPeakFingerprintAnnotationScoreInitialiser method getFingerprintGroup.

protected FingerprintGroup[] getFingerprintGroup(String[] splittedLine) {
    FingerprintGroup[] groups = new FingerprintGroup[(splittedLine.length - 1) / 2];
    int index = 0;
    for (int i = 1; i < splittedLine.length; i += 2) {
        double count = Double.parseDouble(splittedLine[i]);
        FingerprintGroup newGroup = new FingerprintGroup(count);
        newGroup.setNumberObserved((int) count);
        newGroup.setFingerprint(splittedLine[i + 1]);
        groups[index] = newGroup;
        index++;
    }
    return groups;
}

Example 5 with FingerprintGroup

use of de.ipbhalle.metfraglib.substructure.FingerprintGroup in project MetFragRelaunched by ipb-halle.

the class AutomatedPeakFingerprintAnnotationScoreInitialiser method initScoreParameters.

@Override
public void initScoreParameters(Settings settings) throws Exception {
    if (!settings.containsKey(VariableNames.PEAK_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME) || settings.get(VariableNames.PEAK_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME) == null) {
        MassToFingerprintGroupListCollection peakToFingerprintGroupListCollection = new MassToFingerprintGroupListCollection();
        DefaultPeakList peakList = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
        Double mzppm = (Double) settings.get(VariableNames.RELATIVE_MASS_DEVIATION_NAME);
        Double mzabs = (Double) settings.get(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME);
        BufferedReader breader = null;
        java.io.InputStream is = null;
        if (settings.containsKey(VariableNames.FINGERPRINT_PEAK_ANNOTATION_FILE_NAME) && settings.get(VariableNames.FINGERPRINT_PEAK_ANNOTATION_FILE_NAME) != null) {
            breader = new BufferedReader(new FileReader(new File((String) settings.get(VariableNames.FINGERPRINT_PEAK_ANNOTATION_FILE_NAME))));
        } else {
            String filename = "peak_annotations_neg.txt";
            if ((Boolean) settings.get(VariableNames.IS_POSITIVE_ION_MODE_NAME))
                filename = "peak_annotations_pos.txt";
            is = AutomatedPeakFingerprintAnnotationScoreInitialiser.class.getResourceAsStream("/" + filename);
            breader = new java.io.BufferedReader(new java.io.InputStreamReader(is));
        }
        String line = "";
        int numMatchedObservationsMerged = 0;
        java.util.HashMap<Double, MassToFingerprintGroupList> mergedFingerprintGroupLists = new java.util.HashMap<Double, MassToFingerprintGroupList>();
        this.setPseudoCountValues(settings);
        String nonMatchedMassesString = breader.readLine().trim();
        int numNonMatchElements = 0;
        int numNonMatchOccurrences = 0;
        if (!nonMatchedMassesString.equals("NA")) {
            String[] tmp = nonMatchedMassesString.split(";");
            numNonMatchElements = tmp.length;
            for (int k = 0; k < tmp.length; k++) {
                String[] tmp2 = tmp[k].split(":");
                int count = 1;
                Double newMass = Double.parseDouble(tmp2[0]);
                if (tmp2.length == 2)
                    count = Integer.parseInt(tmp2[1]);
                numNonMatchOccurrences += count;
                Double matchedMass = peakList.getBestMatchingMass(newMass, mzppm, mzabs);
                if (matchedMass == null && newMass > peakList.getMaximumMassValue())
                    break;
                if (matchedMass != null) {
                    FingerprintGroup group = new FingerprintGroup(1.0);
                    group.setNumberObserved(count);
                    group.setFingerprint("0");
                    if (mergedFingerprintGroupLists.containsKey(matchedMass)) {
                        MassToFingerprintGroupList currentGroupList = mergedFingerprintGroupLists.get(matchedMass);
                        FingerprintGroup curGroup = currentGroupList.getElementByFingerprint(group.getFingerprint());
                        if (curGroup == null)
                            currentGroupList.addElement(group);
                        else {
                            numNonMatchElements--;
                            curGroup.setNumberObserved(curGroup.getNumberObserved() + group.getNumberObserved());
                            curGroup.setProbability(curGroup.getProbability() + group.getProbability());
                        }
                    } else {
                        MassToFingerprintGroupList currentGroupList = new MassToFingerprintGroupList(matchedMass);
                        currentGroupList.addElement(group);
                        mergedFingerprintGroupLists.put(matchedMass, currentGroupList);
                    }
                }
            }
        }
        while ((line = breader.readLine()) != null) {
            line = line.trim();
            if (line.length() == 0)
                continue;
            if (line.startsWith("#"))
                continue;
            if (line.startsWith("SUMMARY")) {
                String[] tmp = line.split("\\s+");
                // sum overall occurrences
                settings.set(VariableNames.PEAK_FINGERPRINT_DENOMINATOR_COUNT_NAME, Double.parseDouble(tmp[2]) + numNonMatchOccurrences);
                // number different peak pairs matched
                settings.set(VariableNames.PEAK_FINGERPRINT_MATCHED_TUPLE_COUNT_NAME, Double.parseDouble(tmp[1]) - numMatchedObservationsMerged);
                // number different peak pairs non-matched
                settings.set(VariableNames.PEAK_FINGERPRINT_NON_MATCHED_TUPLE_COUNT_NAME, (double) numNonMatchElements);
                continue;
            }
            String[] tmp = line.split("\\s+");
            Double peak = Double.parseDouble(tmp[0]);
            // find matching peak in spectrum
            Double matchedMass = peakList.getBestMatchingMass(peak, mzppm, mzabs);
            if (matchedMass != null) {
                FingerprintGroup[] groups = this.getFingerprintGroup(tmp);
                if (mergedFingerprintGroupLists.containsKey(matchedMass)) {
                    MassToFingerprintGroupList currentGroupList = mergedFingerprintGroupLists.get(matchedMass);
                    for (int i = 0; i < groups.length; i++) {
                        FingerprintGroup curGroup = currentGroupList.getElementByFingerprint(groups[i].getFingerprint());
                        if (curGroup == null)
                            currentGroupList.addElement(groups[i]);
                        else {
                            if (curGroup.getFingerprint().getSize() != 1)
                                numMatchedObservationsMerged++;
                            curGroup.setNumberObserved(curGroup.getNumberObserved() + groups[i].getNumberObserved());
                            curGroup.setProbability(curGroup.getProbability() + groups[i].getProbability());
                        }
                    }
                } else {
                    MassToFingerprintGroupList currentGroupList = new MassToFingerprintGroupList(matchedMass);
                    for (int i = 0; i < groups.length; i++) currentGroupList.addElement(groups[i]);
                    mergedFingerprintGroupLists.put(matchedMass, currentGroupList);
                }
            }
        }
        java.util.Iterator<Double> it = mergedFingerprintGroupLists.keySet().iterator();
        while (it.hasNext()) {
            peakToFingerprintGroupListCollection.addElementSorted(mergedFingerprintGroupLists.get(it.next()));
        }
        breader.close();
        settings.set(VariableNames.PEAK_TO_FINGERPRINT_GROUP_LIST_COLLECTION_NAME, peakToFingerprintGroupListCollection);
    }
}