Examples with LocalPSVDatabase de.ipbhalle.metfraglib.database.LocalPSVDatabase used on opensource projects

Example 1 with LocalPSVDatabase

use of de.ipbhalle.metfraglib.database.LocalPSVDatabase in project MetFragRelaunched by ipb-halle.

the class DownloadEntriesFromPubChem method downloadFromCandidateFile.

public static void downloadFromCandidateFile(String filenameIn, String filenameOut) {
    MetFragGlobalSettings settingsIn = new MetFragGlobalSettings();
    settingsIn.set(VariableNames.LOCAL_DATABASE_PATH_NAME, filenameIn);
    LocalPSVDatabase dbIn = new LocalPSVDatabase(settingsIn);
    ArrayList<String> identifiers = null;
    try {
        identifiers = dbIn.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    CandidateList candidates = dbIn.getCandidateByIdentifier(identifiers);
    String[] ids = new String[candidates.getNumberElements()];
    for (int i = 0; i < ids.length; i++) ids[i] = candidates.getElement(i).getIdentifier();
    MetFragGlobalSettings settingsPubChem = new MetFragGlobalSettings();
    settingsPubChem.set(VariableNames.PRECURSOR_DATABASE_IDS_NAME, ids);
    OnlineExtendedPubChemDatabase pubchemDB = new OnlineExtendedPubChemDatabase(settingsPubChem);
    try {
        identifiers = pubchemDB.getCandidateIdentifiers();
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    CandidateList candidatesPubChem = null;
    try {
        candidatesPubChem = pubchemDB.getCandidateByIdentifier(identifiers);
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    for (int i = 0; i < candidatesPubChem.getNumberElements(); i++) {
        String identifier = candidatesPubChem.getElement(i).getIdentifier();
        try {
            ICandidate currentCandidate = dbIn.getCandidateByIdentifier(identifier);
            currentCandidate.setProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME, candidatesPubChem.getElement(i).getProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME));
            currentCandidate.setProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME, candidatesPubChem.getElement(i).getProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME));
        } catch (DatabaseIdentifierNotFoundException e) {
            e.printStackTrace();
        }
    }
    CandidateListWriterPSV writer = new CandidateListWriterPSV();
    String filename = filenameOut.replaceAll(".*\\/", "").replaceAll("\\..*$", "");
    String path = filenameOut.replaceAll(filename + "\\..*$", "");
    try {
        writer.write(candidates, filename, path);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with LocalPSVDatabase

use of de.ipbhalle.metfraglib.database.LocalPSVDatabase in project MetFragRelaunched by ipb-halle.

the class WriteLossAnnotationFile method main.

/*
	 * write annotation file
	 * 
	 * filename - input file name
	 * mzppm
	 * mzabs
	 * probtype - probability type: 1 - P ( s | p ); 2 - P ( p | s ); 3 - P ( p , s ) from s; 4 - P ( p , s ) from p; 5 - P ( s | p ) P ( p | s ) P ( p , s )_s P ( p , s )_p
	 * output - output smarts
	 * outputSMILES - output smiles
	 * occurThresh
	 * 
	 */
public static void main(String[] args) throws MultipleHeadersFoundInInputDatabaseException, Exception {
    java.util.Hashtable<String, String> readParameters = readParameters(args);
    if (!readParameters.containsKey("filename")) {
        System.err.println("filename missing");
        System.exit(1);
    }
    if (!readParameters.containsKey("mzppm")) {
        System.err.println("mzppm missing");
        System.exit(1);
    }
    if (!readParameters.containsKey("mzabs")) {
        System.err.println("mzabs missing");
        System.exit(1);
    }
    if (!readParameters.containsKey("probtype")) {
        System.err.println("probtype missing");
        System.exit(1);
    }
    String filename = readParameters.get("filename");
    Double mzppm = Double.parseDouble(readParameters.get("mzppm"));
    Double mzabs = Double.parseDouble(readParameters.get("mzabs"));
    Integer probabilityType = Integer.parseInt(readParameters.get("probtype"));
    String output = null;
    String outputSmiles = null;
    Integer occurThresh = null;
    if (readParameters.containsKey("output"))
        output = readParameters.get("output");
    if (readParameters.containsKey("outputSMILES"))
        outputSmiles = readParameters.get("outputSMILES");
    if (readParameters.containsKey("occurThresh"))
        occurThresh = Integer.parseInt(readParameters.get("occurThresh"));
    Settings settings = new Settings();
    settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, filename);
    LocalPSVDatabase db = new LocalPSVDatabase(settings);
    java.util.ArrayList<String> ids = db.getCandidateIdentifiers();
    CandidateList candidateList = db.getCandidateByIdentifier(ids);
    // SmilesOfExplPeaks
    PeakToSmartsGroupListCollection peakToSmartGroupListCollection = new PeakToSmartsGroupListCollection();
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate candidate = candidateList.getElement(i);
        String smilesOfExplPeaks = (String) candidate.getProperty("LossSmilesOfExplPeaks");
        String aromaticSmilesOfExplPeaks = (String) candidate.getProperty("LossAromaticSmilesOfExplPeaks");
        smilesOfExplPeaks = smilesOfExplPeaks.trim();
        aromaticSmilesOfExplPeaks = aromaticSmilesOfExplPeaks.trim();
        if (smilesOfExplPeaks.equals("NA") || aromaticSmilesOfExplPeaks.equals("NA"))
            continue;
        String[] pairs = smilesOfExplPeaks.split(";");
        String[] aromaticPairs = aromaticSmilesOfExplPeaks.split(";");
        if (pairs.length != aromaticPairs.length) {
            System.out.println(candidate.getIdentifier() + " " + candidate.getProperty(VariableNames.INCHI_KEY_1_NAME));
            continue;
        }
        for (int k = 0; k < pairs.length; k++) {
            String[] tmp = pairs[k].split(":");
            String[] aromaticTmp = aromaticPairs[k].split(":");
            Double peak = Double.parseDouble(tmp[0]);
            String smiles = null;
            String smarts = null;
            try {
                smiles = tmp[1];
                smarts = aromaticTmp[1];
            } catch (Exception e) {
                continue;
            }
            PeakToSmartsGroupList peakToSmartGroupList = peakToSmartGroupListCollection.getElementByPeak(peak, mzppm, mzabs);
            if (peakToSmartGroupList == null) {
                peakToSmartGroupList = new PeakToSmartsGroupList(peak);
                SmartsGroup obj = new SmartsGroup(0.0, null, null, null);
                obj.addElement(smarts);
                obj.addSmiles(smiles);
                peakToSmartGroupList.addElement(obj);
                peakToSmartGroupListCollection.addElementSorted(peakToSmartGroupList);
            } else {
                peakToSmartGroupList.setPeakmz((peakToSmartGroupList.getPeakmz() + peak) / 2.0);
                SmartsGroup smartsGroup = peakToSmartGroupList.getElementBySmiles(smiles, 1.0);
                if (smartsGroup != null) {
                    smartsGroup.addElement(smarts);
                    smartsGroup.addSmiles(smiles);
                } else {
                    smartsGroup = new SmartsGroup(0.0, null, null, null);
                    smartsGroup.addElement(smarts);
                    smartsGroup.addSmiles(smiles);
                    peakToSmartGroupList.addElement(smartsGroup);
                }
            }
        }
    }
    // test filtering
    if (occurThresh != null)
        peakToSmartGroupListCollection.filterByOccurence(occurThresh);
    peakToSmartGroupListCollection.annotateIds();
    // get absolute numbers of single substructure occurences
    // N^(s)
    int[] substrOccurences = peakToSmartGroupListCollection.calculateSubstructureAbsoluteProbabilities();
    int[] peakOccurences = peakToSmartGroupListCollection.calculatePeakAbsoluteProbabilities();
    // P ( s | p )
    if (probabilityType == 1) {
        // calculate P ( s | p )
        peakToSmartGroupListCollection.updateConditionalProbabilities();
        peakToSmartGroupListCollection.removeDuplicates();
        peakToSmartGroupListCollection.setProbabilityToConditionalProbability_sp();
        peakToSmartGroupListCollection.sortElementsByProbability();
    }
    // P ( p | s )
    if (probabilityType == 2) {
        System.out.println("annotating IDs");
        // calculate P ( p | s )
        peakToSmartGroupListCollection.updateProbabilities(substrOccurences);
        peakToSmartGroupListCollection.removeDuplicates();
        peakToSmartGroupListCollection.setProbabilityToConditionalProbability_ps();
        peakToSmartGroupListCollection.sortElementsByProbability();
    }
    // P ( p , s )_s
    if (probabilityType == 3) {
        System.out.println("annotating IDs");
        // calculate P ( p , s )
        peakToSmartGroupListCollection.updateJointProbabilitiesWithSubstructures(substrOccurences);
        peakToSmartGroupListCollection.removeDuplicates();
        peakToSmartGroupListCollection.setProbabilityToJointProbability();
        peakToSmartGroupListCollection.sortElementsByProbability();
    }
    // P ( p , s )_p
    if (probabilityType == 4) {
        System.out.println("annotating IDs");
        // calculate P ( p , s )
        peakToSmartGroupListCollection.updateJointProbabilitiesWithPeaks(peakOccurences);
        peakToSmartGroupListCollection.removeDuplicates();
        peakToSmartGroupListCollection.setProbabilityToJointProbability();
        peakToSmartGroupListCollection.sortElementsByProbability();
    }
    // P ( s | p ) P ( p | s ) P( s, p )_s
    if (probabilityType == 5) {
        System.out.println("annotating IDs");
        peakToSmartGroupListCollection.updateConditionalProbabilities();
        peakToSmartGroupListCollection.updateProbabilities(substrOccurences);
        peakToSmartGroupListCollection.updateJointProbabilitiesWithSubstructures(substrOccurences);
        peakToSmartGroupListCollection.removeDuplicates();
        peakToSmartGroupListCollection.setProbabilityToConditionalProbability_sp();
        peakToSmartGroupListCollection.sortElementsByProbability();
        if (output == null)
            peakToSmartGroupListCollection.print();
        else {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(output + "_1")));
            bwriter.write(peakToSmartGroupListCollection.toString());
            bwriter.close();
        }
        if (outputSmiles != null) {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(outputSmiles + "_1")));
            bwriter.write(peakToSmartGroupListCollection.toStringSmiles());
            bwriter.close();
        }
        peakToSmartGroupListCollection.setProbabilityToConditionalProbability_ps();
        peakToSmartGroupListCollection.sortElementsByProbability();
        if (output == null)
            peakToSmartGroupListCollection.print();
        else {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(output + "_2")));
            bwriter.write(peakToSmartGroupListCollection.toString());
            bwriter.close();
        }
        if (outputSmiles != null) {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(outputSmiles + "_2")));
            bwriter.write(peakToSmartGroupListCollection.toStringSmiles());
            bwriter.close();
        }
        peakToSmartGroupListCollection.setProbabilityToJointProbability();
        if (output == null)
            peakToSmartGroupListCollection.print();
        else {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(output + "_3")));
            peakToSmartGroupListCollection.sortElementsByProbability();
            bwriter.write(peakToSmartGroupListCollection.toString());
            bwriter.close();
        }
        if (outputSmiles != null) {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(outputSmiles + "_3")));
            bwriter.write(peakToSmartGroupListCollection.toStringSmiles());
            bwriter.close();
        }
    }
    if (probabilityType != 5) {
        if (output == null)
            peakToSmartGroupListCollection.print();
        else {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(output)));
            bwriter.write(peakToSmartGroupListCollection.toString());
            bwriter.close();
        }
        if (outputSmiles != null) {
            BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File(outputSmiles)));
            bwriter.write(peakToSmartGroupListCollection.toStringSmiles());
            bwriter.close();
        }
    }
}

Example 3 with LocalPSVDatabase

use of de.ipbhalle.metfraglib.database.LocalPSVDatabase in project MetFragRelaunched by ipb-halle.

the class AddMissingNonExplainedPeaks method main.

public static void main(String[] args) throws Exception {
    String paramfile = args[0];
    String resultfile = args[1];
    String outputfile = args[2];
    Settings settings = getSettings(paramfile);
    settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, resultfile);
    IPeakListReader peakListReader = (IPeakListReader) Class.forName((String) settings.get(VariableNames.METFRAG_PEAK_LIST_READER_NAME)).getConstructor(Settings.class).newInstance(settings);
    SettingsChecker settingsChecker = new SettingsChecker();
    if (!settingsChecker.check(settings)) {
        System.err.println("Problems reading settings");
        return;
    }
    settings.set(VariableNames.PEAK_LIST_NAME, peakListReader.read());
    IDatabase db = null;
    String dbFilename = (String) settings.get(VariableNames.LOCAL_DATABASE_PATH_NAME);
    if (dbFilename.endsWith("psv"))
        db = new LocalPSVDatabase(settings);
    else
        db = new LocalCSVDatabase(settings);
    ArrayList<String> ids = null;
    try {
        ids = db.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    CandidateList candidates = null;
    try {
        candidates = db.getCandidateByIdentifier(ids);
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    if (candidates.getNumberElements() == 0) {
        System.out.println("No candidates found in " + (String) settings.get(VariableNames.LOCAL_DATABASE_PATH_NAME));
        return;
    }
    DefaultPeakList peaklist = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        String explPeaks = (String) candidates.getElement(i).getProperty("ExplPeaks");
        String[] explPeaksArray = explPeaks.split(";");
        Double[] explPeaksMasses = null;
        if (!explPeaks.equals("NA"))
            explPeaksMasses = getDoubleArrayFromPeakList(explPeaksArray);
        String nonExplPeaksString = "";
        for (int k = 0; k < peaklist.getNumberElements(); k++) {
            if (explPeaks.equals("NA")) {
                nonExplPeaksString += ((IPeak) peaklist.getElement(k)).getMass() + ";";
            } else if (!isContained(((IPeak) peaklist.getElement(k)).getMass(), explPeaksMasses)) {
                nonExplPeaksString += ((IPeak) peaklist.getElement(k)).getMass() + ";";
            }
        }
        if (nonExplPeaksString.length() == 0)
            nonExplPeaksString = "NA";
        if (nonExplPeaksString.endsWith(";"))
            nonExplPeaksString = nonExplPeaksString.substring(0, nonExplPeaksString.length() - 1);
        candidates.getElement(i).setProperty("NonExplainedMasses", nonExplPeaksString);
    }
    IWriter writer = null;
    if (outputfile.endsWith("psv"))
        writer = new CandidateListWriterPSV();
    else
        writer = new CandidateListWriterCSV();
    writer.write(candidates, outputfile);
}

Example 4 with LocalPSVDatabase

use of de.ipbhalle.metfraglib.database.LocalPSVDatabase in project MetFragRelaunched by ipb-halle.

the class CombineResultsForAnnotation method getMatchingCandidate.

/**
 * @param metfragFiles
 * @param id
 * @param inchikey1
 * @return
 */
public static ICandidate getMatchingCandidate(File[] metfragFiles, String id, String inchikey1) {
    for (int i = 0; i < metfragFiles.length; i++) {
        if (metfragFiles[i].getName().startsWith(id)) {
            MetFragGlobalSettings settings = new MetFragGlobalSettings();
            settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, metfragFiles[i].getAbsolutePath());
            IDatabase db = null;
            if (metfragFiles[i].getName().endsWith("csv"))
                db = new LocalCSVDatabase(settings);
            else
                db = new LocalPSVDatabase(settings);
            ArrayList<String> identifiers = null;
            try {
                identifiers = db.getCandidateIdentifiers();
            } catch (MultipleHeadersFoundInInputDatabaseException e1) {
                e1.printStackTrace();
            } catch (Exception e1) {
                e1.printStackTrace();
            }
            CandidateList candidates = null;
            try {
                candidates = db.getCandidateByIdentifier(identifiers);
            } catch (Exception e1) {
                // TODO Auto-generated catch block
                e1.printStackTrace();
            }
            for (int ii = 0; ii < candidates.getNumberElements(); ii++) {
                if (((String) candidates.getElement(ii).getProperty(VariableNames.INCHI_KEY_1_NAME)).equals(inchikey1)) {
                    return candidates.getElement(ii);
                }
            }
        }
    }
    return null;
}

Example 5 with LocalPSVDatabase

use of de.ipbhalle.metfraglib.database.LocalPSVDatabase in project MetFragRelaunched by ipb-halle.

the class CollectCommuniesAndFragmentPeaks method main.

public static void main(String[] args) {
    MetFragGlobalSettings settings = new MetFragGlobalSettings();
    settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, args[0]);
    LocalPSVDatabase db = new LocalPSVDatabase(settings);
    java.util.ArrayList<String> ids = null;
    try {
        ids = db.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e1) {
        e1.printStackTrace();
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    CandidateList candidates = db.getCandidateByIdentifier(ids);
    ArrayList<Double> masses = new ArrayList<Double>();
    ArrayList<ArrayList<String>> vector_formulas = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<String>> vector_smiles = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<String>> vector_eawagids = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<Double>> vector_intensities = new ArrayList<ArrayList<Double>>();
    ArrayList<Integer> occurences = new ArrayList<Integer>();
    ArrayList<ArrayList<FingerPrintFragmentCollection>> matchingFragments = new ArrayList<ArrayList<FingerPrintFragmentCollection>>();
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        // System.out.println(candidates.getElement(i).getIdentifier());
        try {
            candidates.getElement(i).initialisePrecursorCandidate();
        } catch (AtomTypeNotKnownFromInputListException e) {
            e.printStackTrace();
        } catch (Exception e) {
            e.printStackTrace();
        }
        CommunityCalculation c = new CommunityCalculation((BitArrayPrecursor) candidates.getElement(i).getPrecursorMolecule());
        DefaultBitArrayFragment[] communityFragments = c.getCommunityFragments();
        String[] formulas = ((String) candidates.getElement(i).getProperties().get("FormulasOfExplPeaks")).split(";");
        String eawagID = (String) candidates.getElement(i).getProperties().get("EawagID");
        String[] smiles = ((String) candidates.getElement(i).getProperties().get("SmilesOfExplPeaks")).split(";");
        String[] explPeaks = ((String) candidates.getElement(i).getProperties().get("ExplPeaks")).split(";");
        boolean debug = false;
        for (int k = 0; k < formulas.length; k++) {
            String[] tmp_formula = formulas[k].split(":");
            String[] tmp_smiles = smiles[k].split(":");
            String[] tmp_intensity = explPeaks[k].split("_");
            if (tmp_formula.length != 2 || tmp_smiles.length != 2 || tmp_intensity.length != 2)
                continue;
            double intensity = Double.parseDouble(tmp_intensity[1]);
            if (intensity < intensityThreshold)
                continue;
            double mass = Double.parseDouble(tmp_formula[0]);
            int index = containsDouble(masses, mass, 5.0, 0.001, debug);
            if (index == -1) {
                int addedIndex = addMassSorted(masses, mass, debug);
                /*
					 * how often we have ssen this peak mass 
					 * here: only once as initial add
					 */
                occurences.add(addedIndex, 1);
                /*
					 * add the fragment
					 */
                addFragmentsAddPositionInitial(candidates.getElement(i).getPrecursorMolecule(), addedIndex, matchingFragments, communityFragments, candidates.getElement(i).getIdentifier());
                ArrayList<String> tmp_formulas = new ArrayList<String>();
                ArrayList<String> tmp_smiless = new ArrayList<String>();
                ArrayList<Double> tmp_intensities = new ArrayList<Double>();
                ArrayList<String> tmp_eawagids = new ArrayList<String>();
                tmp_formulas.add(tmp_formula[1]);
                tmp_smiless.add(tmp_smiles[1]);
                tmp_intensities.add(Double.parseDouble(tmp_intensity[1]));
                tmp_eawagids.add(eawagID);
                vector_formulas.add(addedIndex, tmp_formulas);
                vector_smiles.add(addedIndex, tmp_smiless);
                vector_intensities.add(addedIndex, tmp_intensities);
                vector_eawagids.add(addedIndex, tmp_eawagids);
            } else {
                masses.set(index, (masses.get(index) + mass) / 2.0);
                occurences.set(index, occurences.get(index) + 1);
                addFragmentsAddPosition(candidates.getElement(i).getPrecursorMolecule(), index, matchingFragments, communityFragments, candidates.getElement(i).getIdentifier());
                vector_formulas.get(index).add(tmp_formula[1]);
                vector_smiles.get(index).add(tmp_smiles[1]);
                vector_intensities.get(index).add(Double.parseDouble(tmp_intensity[1]));
                vector_eawagids.get(index).add(eawagID);
            }
        }
    }
    printMasses(masses);
    java.io.BufferedWriter bwriter;
    java.io.BufferedWriter smilesBwriter;
    try {
        smilesBwriter = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[2])));
        bwriter = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[1])));
        for (int i = 0; i < masses.size(); i++) {
            // System.out.println(masses.get(i));
            bwriter.write(masses.get(i) + "");
            bwriter.newLine();
            for (int k = 0; k < vector_formulas.get(i).size(); k++) {
                // System.out.println("\t" + vector_eawagids.get(i).get(k) + ": " + vector_formulas.get(i).get(k) + " " + vector_smiles.get(i).get(k) + " " + vector_intensities.get(i).get(k));
                bwriter.write("\t" + vector_eawagids.get(i).get(k) + ": " + vector_formulas.get(i).get(k) + " " + vector_smiles.get(i).get(k) + " " + vector_intensities.get(i).get(k));
                smilesBwriter.write(vector_smiles.get(i).get(k));
                smilesBwriter.newLine();
                bwriter.newLine();
            }
            // System.out.print("\t");
            bwriter.write("\t");
            for (int k = 0; k < vector_formulas.get(i).size(); k++) {
                // System.out.print(vector_eawagids.get(i).get(k) + ".png ");
                bwriter.write(vector_eawagids.get(i).get(k) + ".png ");
            }
            // System.out.println();
            bwriter.newLine();
            bwriter.newLine();
        // System.out.println();
        }
        bwriter.close();
        smilesBwriter.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
    try {
        java.io.BufferedWriter bwriterComms = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[3])));
        for (int i = 0; i < matchingFragments.size(); i++) {
            bwriterComms.write(masses.get(i) + " " + occurences.get(i));
            bwriterComms.newLine();
            ArrayList<FingerPrintFragmentCollection> collections = matchingFragments.get(i);
            for (int j = 0; j < collections.size(); j++) {
                FingerPrintFragmentCollection collection = collections.get(j);
                bwriterComms.write("\t");
                bwriterComms.write(collection.toString());
                bwriterComms.newLine();
            }
        }
        bwriterComms.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}