package edu.unc.genomics;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.zip.DataFormatException;

import com.beust.jcommander.IStringConverter;
import com.beust.jcommander.ParameterException;

/**
 * @author timpalpant
 *
 */
public class AssemblyConverter implements IStringConverter<Assembly> {
	
	public static final Path ASSEMBLIES_DIR = Paths.get("resources", "assemblies");

	@Override
	public Assembly convert(String value) throws ParameterException {
		// Look for the assembly in the resources/assemblies directory
		Path p = ASSEMBLIES_DIR.resolve(value+".len");
		
		// If it does not exist in the assemblies directory, check if it is a path to a file
		if (!Files.isReadable(p)) {
			PathConverter converter = new PathConverter();
			p = converter.convert(value);
			// If it does not exist, then throw an exception that the assembly cannot be found
			if (!Files.isReadable(p)) {
				throw new ParameterException("Cannot find Assembly file: " + value);
			}
		}
		
		// Attempt to load the assembly from file
		try {
			return new Assembly(p);
		} catch (IOException | DataFormatException e) {
			throw new ParameterException("Error loading Assembly from file: " + p);
		}
	}
	
}