package versusSNP;
import java.util.Locale;
import versusSNP.blast.BlastParser;
import versusSNP.blast.util.CodonTable;
import versusSNP.genome.Genome;
import versusSNP.gui.UICaption;
import versusSNP.io.FastaFile;
import versusSNP.io.ORFFile;
public class Main {
public static void main(String[] args) {
new Parameter();
new UICaption(Locale.ENGLISH);
new Size();
// args = new String[]{"NC_000962", "NC_002755"};
new CodonTable();
if (args.length > 0) {
Genome genome1 = new Genome(args[0]);
new ORFFile().readFile(args[0] + ".txt", genome1);
genome1.sortOrfList();
FastaFile fastaFile1 = new FastaFile();
fastaFile1.readFile(args[0] + ".fasta", genome1);
genome1.attachSequences(fastaFile1.getSequences());
Genome genome2 = new Genome(args[1]);
new ORFFile().readFile(args[1] + ".txt", genome2);
genome2.sortOrfList();
FastaFile fastaFile2 = new FastaFile();
fastaFile2.readFile(args[1] + ".fasta", genome2);
genome2.attachSequences(fastaFile2.getSequences());
BlastParser parser = new BlastParser();
parser.parse(args[0] + "-" + args[1]);
genome1.attachBlastSets(parser.getBlastList(), genome2, true);
genome1.printSNPSummary(genome2);
} else {
new VersusSNP().setVisible(true);
}
}
}