package testalter;

import es.uvigo.ei.sing.alter.converter.Converter;
import es.uvigo.ei.sing.alter.converter.DefaultFactory;
import es.uvigo.ei.sing.alter.parser.ParseException;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;

public class TestAlter {

	public static void main(String[] args) throws IOException {
		Converter converter = new DefaultFactory().getConverter(
            "Linux", 	// Input operating system (Linux, MacOS or Windows)
			"clustal", 	// Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)
			"NEXUS",	// Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
			false,		// Autodetect format (other input options are omitted)
			false,		// Collapse sequences to haplotypes
			true,		// Treat gaps as missing data when collapsing
			false,		// Count missing data as differences when collapsing
			0,			// Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0)
			"windows",	// Output operating system (Linux, MacOS or Windows)
			"general",	// Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,
						// ProtTest, RAxML, TCS, CodABC,
						// BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,
						// MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)
			"aln",  	// Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
			false,		// Low case output
			false,		// Output residue numbers (only ALN format)
			false,		// Sequential output (only NEXUS and PHYLIP formats)
			false,		// Output match characters
			"MyConverterApp" // identifier for log messages
		);


		try {
			String inputSequence = new String(Files.readAllBytes(Paths.get("input.nexus")));

			String converted = converter.convert(inputSequence);

			System.out.println("converted file:");
			System.out.println(converted);

		} catch (ParseException e) {
			System.err.println("the input file seems to contain errors");
			e.printStackTrace();
		}

	}
}