biopax paxtools

aaa.java

package bar;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Set;

import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.Protein;

public class aaa {

	public static void main(String[] args) throws FileNotFoundException {
		FileInputStream fin = new FileInputStream(
				"/Users/knishida/biopax-level3.owl");
		BioPAXIOHandler handler = new SimpleIOHandler();
		Model model = handler.convertFromOWL(fin);

		Set<Protein> proteinSet = model.getObjects(Protein.class);

		File file = new File("aaa.tsv");
		try {
			FileWriter filewriter = new FileWriter(file);
			filewriter.write("availability\tcomponent\tcontrollerof\tdatasource\tentityref\txref\tlongname\tcomment\tname\n");
			for (Protein currentProtein : proteinSet) {
				filewriter.write(currentProtein.getAvailability() + "\t"
//						+ currentProtein.getCellularLocation().toString() + "\t"
						+ currentProtein.getComponentOf().toString() + "\t"
						+ currentProtein.getControllerOf().toString() + "\t"
						+ currentProtein.getDataSource().toString() + "\t"
						+ currentProtein.getEntityReference().getXref() + "\t"
						+ currentProtein.getXref().toString() + "\t"
						+ currentProtein.getStandardName() + "\t"
						+ currentProtein.getComment() + "\t"
						+ currentProtein.getDisplayName() + "\n");
			}
			filewriter.close();
		} catch (IOException e) {
			e.printStackTrace();
		}

		System.out.println("OK");
	}
}