Sto utilizzando le librerie di Bio4j, immaginate che io abbia un codice simile a questo:

codice:
package com.era7.bioinfo.bio4j.codesamples;
 
import com.era7.bioinfo.bio4j.neo4j.model.nodes.ProteinNode;
import com.era7.bioinfo.bio4j.neo4j.model.util.Bio4jManager;
import com.era7.bioinfo.bio4j.neo4j.model.util.NodeRetriever;
 
/**
 *
 * Retrieves basic gene information for a protein
 *
 * @author Pablo Pareja Tobes <ppareja@era7.com>
 */
public class GetGenesInfo {
 
    /**
     * @param args Just two arguments (DB folder and protein accession)
     */
    public static void main(String[] args) {
 
        if (args.length != 2) {
            System.out.println("The program expects two parameters: \n"
                    + "1. Bio4j DB folder\n"
                    + "2. Protein accession\n");
        } else {
 
            String inputSt = args[1];
 
            Bio4jManager manager = null;
 
            try {
 
                //--creating manager and node retriever----
                manager = new Bio4jManager(args[0]);
                NodeRetriever nodeRetriever = new NodeRetriever(manager);
 
                //--------------------------------------------------------------
                //-----retrieving protein by its accession---------
 
                ProteinNode protein = nodeRetriever.getProteinNodeByAccession(inputSt);
 
                //checking there's a protein with the accession provided...
                if (protein == null) {
                    System.out.println("There's no protein with the accession " + inputSt);
                } else {
                    System.out.println("Protein found: \n" + inputSt);
                    
                    //----getting gene names-----                
                    String[] geneNames = protein.getGeneNames();
                    System.out.println("Gene names: ");
                    for (String string : geneNames) {
                        System.out.println(string + ",");
                    }
                }
                //--------------------------------------------------------------
 
 
            } catch (Exception e) {
                //deal somehow with the exception
            } finally {
 
                //---closing the manager----
                manager.shutDown();
 
            }
 
        }
    }
}
Come potete vedere ci sono queste istruzioni:

codice:
if (args.length != 2) {
            System.out.println("The program expects two parameters: \n"
                    + "1. Bio4j DB folder\n"
                    + "2. Protein accession\n");
        } else {
Il problema č che io non riesco a trovare la cartella del database....potreste provare a vedere se capite qualcosa?

Bio4j č scaricabile da qui:

https://github.com/bio4j

Ho scaricato dal primo link.