Examples with SimpleDataPoint net.sf.mzmine.datamodel.impl.SimpleDataPoint used on opensource projects

Example 56 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class GnpsMgfParser method parse.

@Override
public boolean parse(AbstractTask mainTask, File dataBaseFile) throws IOException {
    logger.info("Parsing mgf spectral library " + dataBaseFile.getAbsolutePath());
    // BEGIN IONS
    // meta data
    // SCANS=1 .... n (the scan ID; could be used to put all spectra of the same entry together)
    // data
    // END IONS
    int correct = 0;
    State state = State.WAIT_FOR_META;
    Map<DBEntryField, Object> fields = new EnumMap<>(DBEntryField.class);
    List<DataPoint> dps = new ArrayList<>();
    int sep = -1;
    // create db
    try (BufferedReader br = new BufferedReader(new FileReader(dataBaseFile))) {
        for (String l; (l = br.readLine()) != null; ) {
            // main task was canceled?
            if (mainTask != null && mainTask.isCanceled()) {
                return false;
            }
            try {
                if (l.length() > 1) {
                    // meta data start?
                    if (state.equals(State.WAIT_FOR_META)) {
                        if (l.equalsIgnoreCase("BEGIN IONS")) {
                            fields = new EnumMap<>(fields);
                            dps.clear();
                            state = State.META;
                        }
                    } else {
                        if (l.equalsIgnoreCase("END IONS")) {
                            // add entry and reset
                            if (fields.size() > 1 && dps.size() > 1) {
                                SpectralDBEntry entry = new SpectralDBEntry(fields, dps.toArray(new DataPoint[dps.size()]));
                                // add and push
                                addLibraryEntry(entry);
                                correct++;
                            }
                            state = State.WAIT_FOR_META;
                        } else if (l.toLowerCase().startsWith("scans")) {
                            // belongs to the previously created entry and is another spectrum
                            // data starts
                            state = State.DATA;
                        } else {
                            switch(state) {
                                case WAIT_FOR_META:
                                    // wait for next entry
                                    break;
                                case DATA:
                                    String[] data = l.split("\t");
                                    dps.add(new SimpleDataPoint(Double.parseDouble(data[0]), Double.parseDouble(data[1])));
                                    break;
                                case META:
                                    sep = l.indexOf('=');
                                    if (sep != -1 && sep < l.length() - 1) {
                                        DBEntryField field = DBEntryField.forMgfID(l.substring(0, sep));
                                        if (field != null) {
                                            String content = l.substring(sep + 1, l.length());
                                            if (!content.isEmpty()) {
                                                try {
                                                    Object value = field.convertValue(content);
                                                    // name
                                                    if (field.equals(DBEntryField.NAME)) {
                                                        String name = ((String) value);
                                                        int lastSpace = name.lastIndexOf(' ');
                                                        if (lastSpace != -1 && lastSpace < name.length() - 2) {
                                                            String adductCandidate = name.substring(lastSpace + 1);
                                                            // check for valid adduct with the adduct parser from export
                                                            // use as adduct
                                                            String adduct = AdductParser.parse(adductCandidate);
                                                            if (adduct != null && !adduct.isEmpty())
                                                                fields.put(DBEntryField.ION_TYPE, adduct);
                                                        }
                                                    }
                                                    fields.put(field, value);
                                                } catch (Exception e) {
                                                    logger.log(Level.WARNING, "Cannot convert value type of " + content + " to " + field.getObjectClass().toString(), e);
                                                }
                                            }
                                        }
                                    }
                                    break;
                            }
                        }
                    }
                }
            } catch (Exception ex) {
                logger.log(Level.WARNING, "Error for entry", ex);
                state = State.WAIT_FOR_META;
            }
        }
        // finish and process all entries
        finish();
        return true;
    }
}

Example 57 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class GnpsJsonParser method getDataPoints.

/**
 * Data points or null
 *
 * @param main
 * @return
 */
public DataPoint[] getDataPoints(JsonObject main) {
    JsonArray data = main.getJsonArray("peaks");
    if (data == null)
        return null;
    DataPoint[] dps = new DataPoint[data.size()];
    try {
        for (int i = 0; i < data.size(); i++) {
            double mz = data.getJsonArray(i).getJsonNumber(0).doubleValue();
            double intensity = data.getJsonArray(i).getJsonNumber(1).doubleValue();
            dps[i] = new SimpleDataPoint(mz, intensity);
        }
        return dps;
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Cannot convert DP values to doubles", e);
        return null;
    }
}

Example 58 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class JdxParser method parse.

@Override
public boolean parse(AbstractTask mainTask, File dataBaseFile) throws IOException {
    logger.info("Parsing jdx spectral library " + dataBaseFile.getAbsolutePath());
    boolean isData = false;
    Map<DBEntryField, Object> fields = new EnumMap<>(DBEntryField.class);
    List<DataPoint> dps = new ArrayList<>();
    // create db
    int sep = -1;
    try (BufferedReader br = new BufferedReader(new FileReader(dataBaseFile))) {
        for (String l; (l = br.readLine()) != null; ) {
            // main task was canceled?
            if (mainTask.isCanceled()) {
                return false;
            }
            try {
                // meta data?
                sep = isData ? -1 : l.indexOf("=");
                if (sep != -1) {
                    DBEntryField field = DBEntryField.forJdxID(l.substring(0, sep));
                    if (field != null) {
                        String content = l.substring(sep + 1, l.length());
                        if (content.length() > 0) {
                            try {
                                Object value = field.convertValue(content);
                                fields.put(field, value);
                            } catch (Exception e) {
                                logger.log(Level.WARNING, "Cannot convert value type of " + content + " to " + field.getObjectClass().toString(), e);
                            }
                        }
                    }
                } else {
                    // data?
                    String[] dataPairs = l.split(" ");
                    for (String dataPair : dataPairs) {
                        String[] data = dataPair.split(",");
                        if (data.length == 2) {
                            try {
                                dps.add(new SimpleDataPoint(Double.parseDouble(data[0]), Double.parseDouble(data[1])));
                                isData = true;
                            } catch (Exception e) {
                            }
                        }
                    }
                }
                if (l.contains("END")) {
                    // row with END
                    // add entry and reset
                    SpectralDBEntry entry = new SpectralDBEntry(fields, dps.toArray(new DataPoint[dps.size()]));
                    fields = new EnumMap<>(fields);
                    dps.clear();
                    addLibraryEntry(entry);
                    // reset
                    isData = false;
                }
            } catch (Exception ex) {
                logger.log(Level.WARNING, "Error for entry", ex);
            }
        }
    }
    // finish and push last entries
    finish();
    return true;
}