MmDatabase.java

package uk.ac.ebi.ep.centralservice.helper;

/**
 * Databases included in the mega-map (or encountered in some way during the
 * process of building it).
 *
 * @author rafa
 *
 */
public enum MmDatabase {

    Agricola("Agricola citation"),
    ArrayExpressAtlas,
    BRENDA,
    Beilstein("Beilstein Registry Number"),
    BioModels,
    CAS("CAS Registry Number"),
    COMe,
    ChEBI,
    ChEMBL("ChEMBL COMPOUND", "ChEMBL-Compound"),
    ChEMBL_Activity("ChEMBL-Activity"),
    ChEMBL_Target("ChEMBL.Target"),
    Chinese_Abstracts("Chinese Abstracts citation"),
    DrugBank,
    EC,
    EFO,
    Gmelin("Gmelin Registry Number"),
    Golm,
    HMDB,
    IEDB,
    IntAct,
    IntEnz,
    KEGG_COMPOUND("KEGG COMPOUND"),
    KEGG_DRUG("KEGG DRUG"),
    KEGG_GLYCAN("KEGG GLYCAN"),
    Linnean, // taxonomy
    LIPID_MAPS_class("LIPID MAPS class"),
    LIPID_MAPS_instance("LIPID MAPS instance"),
    MeSH,
    MetaCyc,
    MolBase,
    NMRShiftDB,
    OMIM,
    PDB("PDBe"),
    PDBeChem("MSDCHEM"),
    Patent,
    PubChem,
    PubMed("PubMed citation"),
    RESID,
    Reactome,
    Reaxys("Reaxys Registry Number"),
    Rhea,
    SABIO_RK("SABIO-RK"),
    SwissProt("Swiss-Prot"),
    TrEMBL,
    UM_BBD_compID("UM-BBD compID"),
    UniProt,
    WebElements,
    Wikipedia;

    /**
     * Any synonyms for the database.
     */
    private final String[] synonyms;

    private MmDatabase(String... synonyms) {
        this.synonyms = synonyms;
    }

    public String getIdField() {
        return name() + "_ID";
    }

    public String getNameField() {
        return name() + "_NAME";
    }

    public String getAccessionField() {
        return name() + "_ACCESSION";
    }

    /**
     * Parses a string into a MmDatabase value. This method is more flexible
     * than <code>valueOf</code>, accepting database synonyms (ex. 'TrEMBL' will
     * be parsed as {@link #UniProt}) and ignoring letter case.
     *
     * @param s
     * @return a MmDatabase, or <code>null</code> if no match is found.
     */
    public static MmDatabase parse(String s) {
        MmDatabase result = null;
        result = MmDatabase.valueOf(s);

        dbLoop:
        for (MmDatabase db : values()) {
            // Try ignoring case:
            if (db.name().equalsIgnoreCase(s)) {
                result = db;
                break;
            }
            // Try to guess from synonyms:
            if (db.synonyms != null) {
                for (String synonym : db.synonyms) {
                    if (synonym.equalsIgnoreCase(s)) {
                        result = db;
                        break dbLoop;
                    }
                }
            }
        }
        return result;
    }
}