InterMineGff3Loader

package org.intermine.bio.dataconversion;

import org.intermine.bio.io.gff3.GFF3Record;
import org.intermine.metadata.Model;
import org.intermine.xml.full.Item;
import java.util.List;
import java.util.ArrayList;
import org.intermine.objectstore.ObjectStoreException;

public class GffBfcGFF3RecordHandler extends GFF3RecordHandler
{

	private String geneRefId = null;

	/**
     	* Create a new GffBfcGFF3RecordHandler for the given data model.
     	* @param model the model for which items will be created
     	*/
	public GffBfcGFF3RecordHandler (Model model) {
	super(model);
	//Creation des liens entre objets
	refsAndCollections.put("Exon", "transcripts");
	refsAndCollections.put("MRNA", "gene");
	refsAndCollections.put("Protein", "gene");
	}


    @Override
    public void process(GFF3Record record) {

        Item feature = getFeature();
        //Recuperation du contenu de Note dans un attribut "product"
        if (record.getAttributes().containsKey("Note")) 
        {
	List<String> noteList = record.getAttributes().get("Note");
	if (! noteList.isEmpty())
	{	
		String product = noteList.get(0);
		feature.setAttribute("product", product);}
	}

	String clsName = feature.getClassName();
	if ("Gene".equals(clsName)) 
	{
		//Stockage du dernier ID de gene rencontre
		geneRefId = record.getAttributes().get("ID").get(0);
	}
	else if ("CDS".equals(clsName)) 
	{
		//Recuperation de l'item du dernier gene rencontre
		//  --> il faut son primaryId et son organisme 
		Item gene = super.converter.createItem("Gene");
		gene.setAttribute("primaryIdentifier", geneRefId);
		gene.setReference("organism", super.getOrganism());
		//Creation d'un item protein associe
		Item protein = super.converter.createItem("Protein");
		protein.setAttribute("primaryIdentifier", record.getAttributes().get("Name").get(0));
		gene.addToCollection("proteins", protein);
		//Stockage de cet item (la feature en cours est automatiquement "storée"
		// mais ce n'est pas le cas pour l'item créé à la volée 
		try { super.converter.store(protein); } catch (ObjectStoreException e) { e.printStackTrace();}
		//Lien CDS (la feature en cours <-> protein
		feature.setReference("protein", protein);
		}
	}
}