package driver;

import dna.Data;
import dna.Gene;
import fileIO.ChainLine;

public class Translator2 {
	
	
	public static void main(String[] args){
		
		int from=Gene.toBuild(args[0]);
		int to=Gene.toBuild(args[1]);

		if(from==18){from=36;}
		if(from==19){from=37;}
		if(to==18){to=36;}
		if(to==19){to=37;}
		assert(from!=to);
		assert(from==36 || from==37);
		assert(to==36 || to==37);
		
		int chrom=Gene.toChromosome(args[2]);
		
		ChainLine[][] lines=Data.getChainLines(from, to);

		for(int i=3; i<args.length; i++){
			int loc=Integer.parseInt(args[i]);
			int[] result=ChainLine.translate(loc, lines[chrom]);
			System.out.print("(build"+from+", chr"+chrom+", +, "+loc+")  ->  ");
			System.out.println(result==null ? "null" : 
				"(build"+to+", chr"+result[0]+", "+Gene.strandCodes[result[1]]+", "+result[2]+")");
		}
		
//		Translator2 tr=new Translator2(from, to);
//		
//		ChainLine[] array=lines[chrom];
//		int index=ChainLine.binarySearch(loc, array);
////		if(index<0){return null;}
//		ChainLine cl=array[index];
//		
////		System.out.println(cl);
//		
//		int[] dest=cl.translate(loc);
//		
////		{qChrom, qStrand, qStart+loc-tStart};
//		
//		System.out.println(chrom+", +, "+loc+"   ->   "+dest[0]+", "+Gene.strandCodes[dest[1]]+", "+dest[2]);
	}
	
	/** chrom, strand, loc */
	public static final int[] translate(int fromBuild, int toBuild, int chrom, int strand, int loc){
		ChainLine[][] lines=Data.getChainLines(fromBuild, toBuild);
		int[] result=ChainLine.translate(loc, lines[chrom]);
		if(result==null){return null;}
		int strand2=result[1];
		if(strand2==strand){
			result[1]=Gene.PLUS;
		}else{
			result[1]=Gene.MINUS;
		}
		return result;
	}
	
}
