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package fileIO;
import dna.Data;
import dna.Gene;
import shared.Shared;
public class ChainLine implements Comparable<ChainLine> {
public static void main(String[] args){
int chrom=Gene.toChromosome(args[0]);
ChainLine[][] lines=ChainBlock.loadChainLines(Data.ROOT_CHAIN+"hg18ToHg19.over.chain");
for(int i=1; i<args.length; i++){
int loc=Integer.parseInt(args[i]);
int[] result=translate(loc, lines[chrom]);
System.out.print(chrom+"\t+\t"+loc+"\t->\t");
System.out.println(result==null ? "null" : result[0]+"\t"+Shared.strandCodes[result[1]]+"\t"+result[2]);
}
}
public ChainLine(int chromT, byte strandT, int startT, int stopT, int chromQ, byte strandQ, int startQ, int stopQ){
tChrom=chromT;
tStrand=strandT;
tStart=startT;
tStop=stopT;
qChrom=chromQ;
qStrand=strandQ;
qStart=startQ;
qStop=stopQ;
}
@Override
public String toString(){
return tChrom+"\t"+Shared.strandCodes[tStrand]+"\t"+tStart+"\t"+tStop+"\t"+
qChrom+"\t"+Shared.strandCodes[qStrand]+"\t"+qStart+"\t"+qStop;
}
public static int binarySearch(int loc, ChainLine[] array){
return binarySearch(loc, array, 0, array.length-1);
}
public static int binarySearch(int loc, ChainLine[] array, int first, int last){
// if(first>=last){
// if(first>last){return -1;}
// assert(first==last && first<array.length);
// return (array[first].tStart<=loc && array[first].tStop>=loc) ? first : -1;
// }
// System.out.println("BinarySearch "+loc+", "+first+", "+last);
if(first>last){return -1;}
int mid=(first+last)/2;
ChainLine midcl=array[mid];
// System.out.println("mid = "+midcl);
if(loc<midcl.tStart){return binarySearch(loc, array, first, mid-1);}
else if(loc>midcl.tStop){return binarySearch(loc, array, mid+1, last);}
return mid;
}
/** Returns {chrom, strand, loc} */
public static int[] translate(int loc, ChainLine[] array){
int index=binarySearch(loc, array);
if(index<0){return null;}
ChainLine cl=array[index];
return cl.translate(loc);
}
public int[] translate(int loc){
if(loc<tStart || loc>tStop){return null;}
// assert(loc>=tStart && loc<=tStop);
if(qChrom<1 || qChrom>25){return null;}
if(qStrand==Shared.PLUS){
return new int[] {qChrom, qStrand, qStart+loc-tStart};
}else{
assert(qStart>=qStop) : this;
return new int[] {qChrom, qStrand, qStart-(loc-tStart)};
}
}
public boolean contains(int a, int b){
assert(b>=a);
return a>=tStart && b<=tStop;
}
public boolean contains(int a){
return a>=tStart && a<=tStop;
}
@Override
public int compareTo(ChainLine other) {
int temp;
temp=tChrom-other.tChrom;
if(temp!=0){return temp;}
assert(tStrand==other.tStrand);
temp=tStart-other.tStart;
if(temp!=0){return temp;}
temp=tStop-other.tStop;
return temp;
}
public int tChrom;
public byte tStrand;
public int tStart;
public int tStop;
public int qChrom;
public byte qStrand;
public int qStart;
public int qStop;
}
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