Examples with DBLink de.unijena.bioinf.chemdb.DBLink used on opensource projects

Example 1 with DBLink

use of de.unijena.bioinf.chemdb.DBLink in project mzmine2 by mzmine.

the class SiriusCompound method loadProps.

/**
 * Construct parameters from SiriusIonAnnotation Amount of params differ, either it is identified
 * by SiriusIdentificationMethod, or also by FingerIdWebMethod
 *
 * @param annotation
 * @return constructed Hashtable
 */
private static Hashtable<String, String> loadProps(final SiriusIonAnnotation annotation) {
    String formula = MolecularFormulaManipulator.getString(annotation.getFormula());
    String siriusScore = String.format("%.4f", annotation.getSiriusScore());
    String name = null;
    /* Put default properties */
    Hashtable<String, String> props = new Hashtable<>(10);
    props.put(PROPERTY_METHOD, "Sirius");
    props.put(PROPERTY_FORMULA, formula);
    props.put("Sirius score", siriusScore);
    /* Check that annotation is processed by FingerIdWebMethod */
    if (annotation.getFingerIdScore() != null) {
        name = annotation.getDescription();
        String inchi = annotation.getInchiKey();
        String smiles = annotation.getSMILES();
        props.put("SMILES", smiles);
        props.put("Inchi", inchi);
        String fingerScore = String.format("%.4f", annotation.getFingerIdScore());
        props.put("FingerId score", fingerScore);
        DBLink[] links = annotation.getDBLinks();
        Set<String> dbnames = new HashSet<>();
        /*
       * DBLinks may contain several links to Pubchem (for example)
       */
        for (DBLink link : links) {
            dbnames.add(link.name);
        }
        String[] dbs = new String[dbnames.size()];
        dbs = dbnames.toArray(dbs);
        for (String db : dbs) props.put(db, "FOUND");
    }
    // Load name param with formula, if FingerId did not identify it
    if (name == null)
        name = formula;
    props.put(PROPERTY_NAME, name);
    return props;
}

Example 2 with DBLink

use of de.unijena.bioinf.chemdb.DBLink in project mzmine2 by mzmine.

the class SiriusCompound method getDBS.

/**
 * @return unique names of the databases
 */
public String[] getDBS() {
    DBLink[] dblinks = getIonAnnotation().getDBLinks();
    if (dblinks == null)
        return null;
    Set<String> dbNames = new TreeSet<String>();
    for (DBLink link : dblinks) dbNames.add(link.name);
    String[] dbs = new String[dbNames.size()];
    dbs = dbNames.toArray(dbs);
    return dbs;
}

Example 3 with DBLink

use of de.unijena.bioinf.chemdb.DBLink in project mzmine2 by mzmine.

the class DBTableModel method addElement.

/**
 * Method unwraps SiriusCompound and retrieves all the DB links Adds DB links one by one into the
 * table
 *
 * @param compound
 */
public void addElement(SiriusCompound compound) {
    SiriusIonAnnotation annotation = compound.getIonAnnotation();
    DBLink[] links = annotation.getDBLinks();
    if (links == null)
        return;
    for (DBLink link : links) {
        compounds.add(new SiriusDBCompound(link.name, link.id));
        fireTableRowsInserted(compounds.size() - 1, compounds.size() - 1);
    }
}