--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/ChainLine.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,125 @@
+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;
+	
+}