Examples with LibraryMetaDataParameters net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.param.LibraryMetaDataParameters used on opensource projects

Example 1 with LibraryMetaDataParameters

use of net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.param.LibraryMetaDataParameters in project mzmine2 by mzmine.

the class GnpsJsonGenerator method generateJSON.

/**
 * Whole JSON entry
 *
 * @param param
 * @param dps
 * @return
 */
public static String generateJSON(LibrarySubmitIonParameters param, DataPoint[] dps) {
    LibraryMetaDataParameters meta = (LibraryMetaDataParameters) param.getParameter(LibrarySubmitIonParameters.META_PARAM).getValue();
    boolean exportRT = meta.getParameter(LibraryMetaDataParameters.EXPORT_RT).getValue();
    JsonObjectBuilder json = Json.createObjectBuilder();
    // tag spectrum from mzmine2
    json.add(DBEntryField.SOFTWARE.getGnpsJsonID(), "mzmine2");
    // ion specific
    Double precursorMZ = param.getParameter(LibrarySubmitIonParameters.MZ).getValue();
    if (precursorMZ != null)
        json.add(DBEntryField.MZ.getGnpsJsonID(), precursorMZ);
    Integer charge = param.getParameter(LibrarySubmitIonParameters.CHARGE).getValue();
    if (charge != null)
        json.add(DBEntryField.CHARGE.getGnpsJsonID(), charge);
    String adduct = param.getParameter(LibrarySubmitIonParameters.ADDUCT).getValue();
    if (adduct != null && !adduct.trim().isEmpty())
        json.add(DBEntryField.ION_TYPE.getGnpsJsonID(), adduct);
    if (exportRT) {
        Double rt = meta.getParameter(LibraryMetaDataParameters.EXPORT_RT).getEmbeddedParameter().getValue();
        if (rt != null)
            json.add(DBEntryField.RT.getGnpsJsonID(), rt);
    }
    // add data points array
    json.add("peaks", genJSONData(dps));
    // add meta data
    for (Parameter<?> p : meta.getParameters()) {
        if (!p.getName().equals(LibraryMetaDataParameters.EXPORT_RT.getName())) {
            String key = p.getName();
            Object value = p.getValue();
            if (value instanceof Double) {
                if (Double.compare(0d, (Double) value) == 0)
                    json.add(key, 0);
                else
                    json.add(key, (Double) value);
            } else if (value instanceof Float) {
                if (Float.compare(0f, (Float) value) == 0)
                    json.add(key, 0);
                else
                    json.add(key, (Float) value);
            } else if (value instanceof Integer)
                json.add(key, (Integer) value);
            else {
                if (value == null || (value instanceof String && ((String) value).isEmpty()))
                    value = "N/A";
                json.add(key, value.toString());
            }
        }
    }
    // return Json.createObjectBuilder().add("spectrum", json.build()).build().toString();
    return json.build().toString();
}

Example 2 with LibraryMetaDataParameters

use of net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.param.LibraryMetaDataParameters in project mzmine2 by mzmine.

the class MSPEntryGenerator method createMSPEntry.

/**
 * Creates a simple MSP nist format DB entry
 *
 * @param param
 * @param dps
 * @return
 */
public static String createMSPEntry(LibrarySubmitIonParameters param, DataPoint[] dps) {
    LibraryMetaDataParameters meta = (LibraryMetaDataParameters) param.getParameter(LibrarySubmitIonParameters.META_PARAM).getValue();
    boolean exportRT = meta.getParameter(LibraryMetaDataParameters.EXPORT_RT).getValue();
    String ionMode = meta.getParameter(LibraryMetaDataParameters.IONMODE).getValue().equals(Polarity.Positive) ? "P" : "N";
    String def = ": ";
    String br = "\n";
    StringBuilder s = new StringBuilder();
    // tag spectrum from mzmine2
    // ion specific
    s.append(DBEntryField.NAME.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.COMPOUND_NAME).getValue() + br);
    s.append(DBEntryField.INCHIKEY.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.INCHI_AUX).getValue() + br);
    s.append(DBEntryField.MS_LEVEL.getNistMspID() + def + "MS" + meta.getParameter(LibraryMetaDataParameters.MS_LEVEL).getValue() + br);
    s.append(DBEntryField.INSTRUMENT_TYPE.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.INSTRUMENT).getValue() + br);
    s.append(DBEntryField.INSTRUMENT.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.INSTRUMENT_NAME).getValue() + br);
    s.append(DBEntryField.ION_MODE.getNistMspID() + def + ionMode + br);
    s.append(DBEntryField.COLLISION_ENERGY.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.FRAGMENTATION_METHOD).getValue() + br);
    s.append(DBEntryField.FORMULA.getNistMspID() + def + meta.getParameter(LibraryMetaDataParameters.FORMULA).getValue() + br);
    Double exact = meta.getParameter(LibraryMetaDataParameters.EXACT_MASS).getValue();
    if (exact != null)
        s.append(DBEntryField.EXACT_MASS.getNistMspID() + def + exact + br);
    Double precursorMZ = param.getParameter(LibrarySubmitIonParameters.MZ).getValue();
    if (precursorMZ != null)
        s.append(DBEntryField.MZ.getNistMspID() + def + param.getParameter(LibrarySubmitIonParameters.MZ).getValue() + br);
    String adduct = param.getParameter(LibrarySubmitIonParameters.ADDUCT).getValue();
    if (adduct != null && !adduct.trim().isEmpty())
        s.append(DBEntryField.ION_TYPE.getNistMspID() + def + param.getParameter(LibrarySubmitIonParameters.ADDUCT).getValue() + br);
    if (exportRT) {
        Double rt = meta.getParameter(LibraryMetaDataParameters.EXPORT_RT).getEmbeddedParameter().getValue();
        if (rt != null)
            s.append(DBEntryField.RT.getNistMspID() + def + rt + br);
    }
    // num peaks and data
    s.append(DBEntryField.NUM_PEAKS.getNistMspID() + def + dps.length + br);
    NumberFormat mzForm = new DecimalFormat("0.######");
    for (DataPoint dp : dps) {
        s.append(mzForm.format(dp.getMZ()) + " " + dp.getIntensity() + br);
    }
    s.append(br);
    return s.toString();
}