Examples with CandidateList de.ipbhalle.metfraglib.list.CandidateList used on opensource projects

Example 6 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class HDCandidateListWriterPSV method writeFile.

public boolean writeFile(File file, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        int countExplainedPeaks = 0;
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (settings != null)
            scoredCandidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        scoredCandidate.initialisePrecursorCandidate();
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
        }
        String peaksExplained = "";
        String sumFormulasOfFragmentsExplainedPeaks = "";
        if (scoredCandidate.getMatchList() != null) {
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + "_" + intensity + ";";
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                sumFormulasOfFragmentsExplainedPeaks += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + ":" + formula + ";";
            }
            if (sumFormulasOfFragmentsExplainedPeaks.length() != 0)
                sumFormulasOfFragmentsExplainedPeaks = sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1);
            if (peaksExplained.length() != 0)
                peaksExplained = peaksExplained.substring(0, peaksExplained.length() - 1);
            if (peaksExplained.length() == 0)
                peaksExplained = "NA";
            if (sumFormulasOfFragmentsExplainedPeaks.length() == 0)
                sumFormulasOfFragmentsExplainedPeaks = "NA";
            scoredCandidate.setProperty(VariableNames.EXPLAINED_PEAKS_COLUMN, peaksExplained);
            scoredCandidate.setProperty(VariableNames.FORMULAS_OF_PEAKS_EXPLAINED_COLUMN, sumFormulasOfFragmentsExplainedPeaks);
            scoredCandidate.setProperty(VariableNames.NUMBER_PEAKS_USED_COLUMN, numberOfPeaksUsed);
            scoredCandidate.setProperty(VariableNames.NUMBER_EXPLAINED_PEAKS_COLUMN, countExplainedPeaks);
        }
    }
    java.util.Hashtable<String, java.util.ArrayList<ICandidate>> hdGroupedCandidates = new java.util.Hashtable<String, java.util.ArrayList<ICandidate>>();
    String[] lines = new String[candidateList.getNumberElements()];
    String heading = "";
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate candidate = candidateList.getElement(i);
        if (hdGroupedCandidates.containsKey((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME)))
            ((java.util.ArrayList<ICandidate>) hdGroupedCandidates.get((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME))).add(candidate);
        else {
            java.util.ArrayList<ICandidate> vec = new java.util.ArrayList<ICandidate>();
            vec.add(candidate);
            hdGroupedCandidates.put((String) candidate.getProperty(VariableNames.HD_GROUP_FLAG_NAME), vec);
        }
        candidate.getProperties().remove(VariableNames.HD_GROUP_FLAG_NAME);
    }
    java.util.ArrayList<String> propertyNames = new java.util.ArrayList<String>();
    java.util.Iterator<?> it = (java.util.Iterator<?>) hdGroupedCandidates.keys();
    while (it.hasNext()) {
        String currentGroup = (String) it.next();
        java.util.ArrayList<ICandidate> vec = hdGroupedCandidates.get(currentGroup);
        int originalCandidate = -1;
        int maxPropertySize = 0;
        // find original candidate properties
        for (int i = 0; i < vec.size(); i++) {
            if (vec.get(i).getProperties().size() > maxPropertySize) {
                originalCandidate = i;
                maxPropertySize = vec.get(i).getProperties().size();
            }
        }
        // fill in missing properties
        java.util.Hashtable<String, Object> properties = vec.get(originalCandidate).getProperties();
        for (int i = 0; i < vec.size(); i++) {
            ICandidate currentCandidate = vec.get(i);
            java.util.Iterator<?> prop_it = (java.util.Iterator<?>) properties.keys();
            while (prop_it.hasNext()) {
                String key = (String) prop_it.next();
                if (!propertyNames.contains(key))
                    propertyNames.add(key);
                if (currentCandidate.getProperty(key) == null)
                    currentCandidate.setProperty(key, properties.get(key));
            }
        }
    }
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (propertyNames.size() >= 1) {
            String key = propertyNames.get(0);
            if (i == 0)
                heading += key;
            lines[i] = "" + checkEmptyProperty(scoredCandidate.getProperty(key), key);
        }
        for (int k = 1; k < propertyNames.size(); k++) {
            String key = propertyNames.get(k);
            if (i == 0)
                heading += "|" + key;
            String prop = checkEmptyProperty(scoredCandidate.getProperty(key), key).toString();
            lines[i] += "|" + prop;
        }
    }
    java.io.BufferedWriter bwriter = new java.io.BufferedWriter(new FileWriter(file));
    bwriter.write(heading);
    bwriter.newLine();
    for (int i = 0; i < lines.length; i++) {
        bwriter.write(lines[i]);
        bwriter.newLine();
    }
    bwriter.close();
    return true;
}

Example 7 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterExtendedFragmentsXLS method convertMoleculesAndFragmentToImages.

/**
 * @param candidateList
 * @return
 */
private List<List<RenderedImage>> convertMoleculesAndFragmentToImages(CandidateList candidateList) throws Exception {
    List<List<RenderedImage>> molImages = new ArrayList<List<RenderedImage>>();
    de.ipbhalle.metfraglib.imagegenerator.StandardSingleStructureImageGenerator imageGenerator = new de.ipbhalle.metfraglib.imagegenerator.StandardSingleStructureImageGenerator();
    imageGenerator.setImageHeight(200);
    imageGenerator.setImageWidth(200);
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        List<RenderedImage> currentList = new ArrayList<RenderedImage>();
        RenderedImage renderedImage = imageGenerator.generateImage(candidateList.getElement(i));
        if (renderedImage != null) {
            currentList.add(renderedImage);
        } else
            currentList.add(new java.awt.image.BufferedImage(imageGenerator.getImageWidth(), imageGenerator.getImageHeight(), java.awt.image.BufferedImage.TYPE_INT_RGB));
        if (renderedImage != null) {
            MatchList matchList = candidateList.getElement(i).getMatchList();
            for (int k = 0; k < matchList.getNumberElements(); k++) {
                currentList.add(imageGenerator.generateImage(candidateList.getElement(i).getPrecursorMolecule(), matchList.getElement(k).getBestMatchedFragment()));
            }
        }
        molImages.add(currentList);
    }
    return molImages;
}

Example 8 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterLossFragmentSmilesPSV method writeFile.

public boolean writeFile(File file, IList list, Settings settings) throws Exception {
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    StringBuilder heading = new StringBuilder();
    this.removeCandidateProperties(candidateList.getElement(0));
    java.util.Enumeration<String> keys = candidateList.getElement(0).getProperties().keys();
    if (keys.hasMoreElements()) {
        String key = keys.nextElement();
        heading.append(key);
    }
    while (keys.hasMoreElements()) {
        String key = keys.nextElement();
        heading.append("|");
        heading.append(key);
    }
    heading.append("|");
    heading.append("ExplPeaks");
    heading.append("|");
    heading.append("FormulasOfExplPeaks");
    heading.append("|");
    heading.append("FragmentFingerprintOfExplPeaks");
    heading.append("|");
    heading.append("NumberPeaksUsed");
    heading.append("|");
    heading.append("NoExplPeaks");
    heading.append("|");
    heading.append("LossFingerprintOfExplPeaks");
    java.io.BufferedWriter bwriter = new java.io.BufferedWriter(new FileWriter(file));
    bwriter.write(heading.toString());
    bwriter.newLine();
    Fingerprint fingerprint = new Fingerprint((String) settings.get(VariableNames.FINGERPRINT_TYPE_NAME));
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        StringBuilder line = new StringBuilder();
        int countExplainedPeaks = 0;
        ICandidate scoredCandidate = candidateList.getElement(i);
        this.removeCandidateProperties(scoredCandidate);
        if (settings != null)
            scoredCandidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        scoredCandidate.initialisePrecursorCandidate();
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
        }
        keys = scoredCandidate.getProperties().keys();
        if (keys.hasMoreElements()) {
            String key = keys.nextElement();
            line.append(scoredCandidate.getProperty(key));
        }
        while (keys.hasMoreElements()) {
            String key = keys.nextElement();
            line.append("|");
            line.append(scoredCandidate.getProperty(key));
        }
        StringBuilder peaksExplained = new StringBuilder();
        StringBuilder sumFormulasOfFragmentsExplainedPeaks = new StringBuilder();
        StringBuilder fingerprintOfFragmentsExplainedPeaks = new StringBuilder();
        if (scoredCandidate.getMatchList() != null) {
            String[] matchedFormulas = new String[scoredCandidate.getMatchList().getNumberElements()];
            double[] correctedMasses = new double[scoredCandidate.getMatchList().getNumberElements()];
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained.append(scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass());
                    peaksExplained.append("_");
                    peaksExplained.append(intensity);
                    peaksExplained.append(";");
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                double mass = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass();
                if ((Boolean) settings.get(VariableNames.CORRECT_MASSES_FOR_FINGERPRINT_ANNOTATION_NAME)) {
                    matchedFormulas[ii] = formula;
                    correctedMasses[ii] = MathTools.round(calculateMassOfFormula(formula));
                    mass = correctedMasses[ii];
                }
                sumFormulasOfFragmentsExplainedPeaks.append(scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass());
                sumFormulasOfFragmentsExplainedPeaks.append(":");
                sumFormulasOfFragmentsExplainedPeaks.append(formula);
                sumFormulasOfFragmentsExplainedPeaks.append(";");
                // get fragment of explained peak
                IFragment frag = scoredCandidate.getMatchList().getElement(ii).getBestMatchedFragment();
                String fp = null;
                try {
                    IAtomContainer con = fingerprint.getNormalizedAtomContainer(scoredCandidate.getPrecursorMolecule(), frag);
                    fp = fingerprint.getNormalizedFingerprint(con);
                } catch (Exception e) {
                    continue;
                }
                fingerprintOfFragmentsExplainedPeaks.append(mass);
                fingerprintOfFragmentsExplainedPeaks.append(":");
                fingerprintOfFragmentsExplainedPeaks.append(fp);
                fingerprintOfFragmentsExplainedPeaks.append(";");
            }
            line.append("|");
            line.append(peaksExplained.length() == 0 ? "NA" : peaksExplained.substring(0, peaksExplained.length() - 1));
            line.append("|");
            line.append(sumFormulasOfFragmentsExplainedPeaks.length() == 0 ? "NA" : sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1));
            line.append("|");
            line.append(fingerprintOfFragmentsExplainedPeaks.length() == 0 ? "NA" : fingerprintOfFragmentsExplainedPeaks.substring(0, fingerprintOfFragmentsExplainedPeaks.length() - 1));
            line.append("|");
            line.append(numberOfPeaksUsed);
            line.append("|");
            line.append(countExplainedPeaks);
            // add loss information
            if (settings != null) {
                String lossesFingerprints = createLossAnnotations(scoredCandidate.getPrecursorMolecule(), scoredCandidate.getMatchList(), settings, correctedMasses, fingerprint);
                line.append("|");
                line.append(lossesFingerprints);
            }
        }
        bwriter.write(line.toString());
        bwriter.newLine();
    }
    bwriter.close();
    return true;
}

Example 9 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class ConvertMultipleMonaMSPtoMetFragRecord method checkEntries.

public static java.util.ArrayList<Entry> checkEntries(java.util.ArrayList<Entry> entries, String addparamsfile) {
    if (entries.size() == 0)
        return entries;
    MetFragGlobalSettings settings;
    try {
        boolean[] inchikey_id_missmatches = new boolean[entries.size()];
        String[] alternative_pubchem_id = new String[entries.size()];
        settings = MetFragGlobalSettings.readSettings(new File(addparamsfile), null);
        LocalMetChemDatabase lmcd = new LocalMetChemDatabase(settings);
        // check inchikeys
        String inchikeyset = "'" + entries.get(0).inchikey.split("-")[0] + "'";
        for (int i = 1; i < entries.size(); i++) {
            inchikeyset += ",'" + entries.get(i).inchikey.split("-")[0] + "'";
        }
        CandidateList candidates = lmcd.getCandidateListByQuery("2", "c.inchi_key_1 in (" + inchikeyset + ")");
        for (int i = 0; i < entries.size(); i++) {
            inchikey_id_missmatches[i] = true;
            boolean inchikeyfound = false;
            String inchikey1 = entries.get(i).inchikey.split("-")[0];
            LinkedList<String> alternative_pubchem_ids = new LinkedList<String>();
            for (int j = 0; j < candidates.getNumberElements(); j++) {
                if (inchikey1.equals((String) candidates.getElement(j).getProperty(VariableNames.INCHI_KEY_1_NAME))) {
                    inchikeyfound = true;
                    alternative_pubchem_ids.add(candidates.getElement(j).getIdentifier() + "|" + candidates.getElement(j).getProperty(VariableNames.INCHI_KEY_3_NAME));
                    if (candidates.getElement(j).getIdentifier().equals(entries.get(i).pubchemcid))
                        inchikey_id_missmatches[i] = false;
                }
            }
            if (!inchikeyfound)
                inchikey_id_missmatches[i] = true;
            if (inchikey_id_missmatches[i] && alternative_pubchem_ids.size() != 0) {
                java.util.Iterator<String> it = alternative_pubchem_ids.iterator();
                while (it.hasNext()) {
                    String currentid = it.next();
                    if (currentid.endsWith("N"))
                        alternative_pubchem_id[i] = currentid.split("\\|")[0];
                }
                if (alternative_pubchem_id[i] == null || alternative_pubchem_id[i].equals(""))
                    alternative_pubchem_id[i] = alternative_pubchem_ids.getFirst().split("\\|")[0];
            }
        }
        String cidString = "";
        for (int i = 0; i < inchikey_id_missmatches.length; i++) {
            if (inchikey_id_missmatches[i]) {
                cidString += "'" + entries.get(i).pubchemcid + "',";
            }
        }
        if (cidString.length() == 0)
            return entries;
        cidString = cidString.substring(0, cidString.length() - 1);
        candidates = lmcd.getCandidateListByQuery("2", "s.accession in (" + cidString + ")");
        for (int i = 0; i < inchikey_id_missmatches.length; i++) {
            if (inchikey_id_missmatches[i]) {
                System.out.println("inchikey pubchemid mismatch found: " + entries.get(i).sampleName + ": " + entries.get(i).inchikey + " " + entries.get(i).pubchemcid);
                boolean cid_found = false;
                for (int j = 0; j < candidates.getNumberElements(); j++) {
                    if (candidates.getElement(j).getIdentifier().equals(entries.get(i))) {
                        entries.get(i).inchikey = (String) candidates.getElement(j).getProperty(VariableNames.INCHI_KEY_1_NAME);
                        cid_found = true;
                        break;
                    }
                }
                if (!cid_found) {
                    if (alternative_pubchem_id[i] != null && !alternative_pubchem_id[i].equals("")) {
                        entries.get(i).pubchemcid = alternative_pubchem_id[i];
                        cid_found = true;
                    }
                }
                if (cid_found) {
                    System.out.println(" corrected " + entries.get(i).inchikey + " " + entries.get(i).pubchemcid);
                    inchikey_id_missmatches[i] = false;
                }
            }
        }
        // prepare new entry vector
        java.util.ArrayList<Entry> newentries = new java.util.ArrayList<Entry>();
        for (int i = 0; i < inchikey_id_missmatches.length; i++) {
            if (!inchikey_id_missmatches[i])
                newentries.add(entries.get(i));
        }
        return newentries;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return null;
}

Example 10 with CandidateList

use of de.ipbhalle.metfraglib.list.CandidateList in project MetFragRelaunched by ipb-halle.

the class ConvertSDFtoCSV method main.

/**
 * @param args
 * @throws CDKException
 */
public static void main(String[] args) throws CDKException {
    IteratingSDFReader reader;
    CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
    CandidateList candidates = new CandidateList();
    try {
        reader = new IteratingSDFReader(new java.io.FileReader(args[0]), DefaultChemObjectBuilder.getInstance());
        while (reader.hasNext()) {
            IAtomContainer molecule = reader.next();
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
            adder.addImplicitHydrogens(molecule);
            AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
            PrecursorCandidate candidate = new PrecursorCandidate((String) molecule.getProperty(VariableNames.INCHI_NAME), (String) molecule.getProperty(VariableNames.IDENTIFIER_NAME));
            java.util.Iterator<Object> keys = molecule.getProperties().keySet().iterator();
            while (keys.hasNext()) {
                String key = (String) keys.next();
                if (molecule.getProperty(key) != null)
                    candidate.setProperty(key, molecule.getProperty(key));
            }
            candidates.addElement(candidate);
        }
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    }
    CandidateListWriterPSV writer = new CandidateListWriterPSV();
    try {
        writer.write(candidates, args[1], args[2]);
    } catch (Exception e) {
        e.printStackTrace();
    }
}