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package driver;
import dna.Data;
import dna.Gene;
import fileIO.ChainLine;
import shared.Shared;
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]+", "+Shared.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]=Shared.PLUS;
}else{
result[1]=Shared.MINUS;
}
return result;
}
}
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