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package driver;
import java.util.ArrayList;
import java.util.Arrays;
import dna.AminoAcid;
import dna.Data;
import fileIO.ChainLine;
import shared.Shared;
import shared.Tools;
import var.VarLine;
import var.Variation;
public class Translator {
public Translator(int from_, int to_){
fromBuild=from_;
toBuild=to_;
lines=Data.getChainLines(fromBuild, toBuild);
}
public VarLine[][] translate(VarLine[][] in){
ArrayList<VarLine>[] alvls=new ArrayList[in.length];
for(int i=0; i<alvls.length; i++){
alvls[i]=new ArrayList<VarLine>();
}
for(VarLine[] vla : in){
if(vla!=null){
for(VarLine vl : vla){
VarLine vl2=translate(vl);
// if(vl.haplotype==1 && (vl.intersects(244821744, 244821748) || (vl2!=null && vl2.intersects(246755120, 246755126)))){
// System.out.println("\n"+vl+"\n->\n"+vl2);
// }
if(vl2!=null){
int chrom=vl2.chromosome;
alvls[chrom].add(vl2);
}
}
}
}
VarLine[][] out=new VarLine[alvls.length][];
for(int i=0; i<alvls.length; i++){
out[i]=alvls[i].toArray(new VarLine[alvls[i].size()]);
Arrays.sort(out[i]);
alvls[i]=null;
}
return out;
}
public Variation[][] translate(Variation[][] in){
ArrayList<Variation>[] alvls=new ArrayList[in.length];
for(int i=0; i<alvls.length; i++){
alvls[i]=new ArrayList<Variation>();
}
for(Variation[] vla : in){
if(vla!=null){
for(Variation vl : vla){
Variation vl2=translate(vl);
if(vl2!=null){
int chrom=vl2.chromosome;
alvls[chrom].add(vl2);
}
}
}
}
Variation[][] out=new Variation[alvls.length][];
for(int i=0; i<alvls.length; i++){
out[i]=alvls[i].toArray(new Variation[alvls[i].size()]);
Arrays.sort(out[i]);
alvls[i]=null;
}
return out;
}
public VarLine translate(VarLine v){
ChainLine[] array=lines[v.chromosome];
int index=ChainLine.binarySearch(v.beginLoc, array);
if(index<0){return null;}
ChainLine cl=array[index];
if(!cl.contains(v.beginLoc, v.endLoc)){return null;}
// System.out.println(cl);
int[] dest1=cl.translate(v.beginLoc);
int[] dest2=cl.translate(v.endLoc);
if(dest1==null || dest2==null){return null;}
VarLine v2=v.clone();
assert(v!=null);
assert(v2!=null) : v;
if(cl.qStrand==Shared.PLUS){
v2.chromosome=(byte)dest1[0];
v2.beginLoc=dest1[2];
v2.endLoc=dest2[2];
}else{
// assert(false) : "TODO";
v2.chromosome=(byte)dest1[0];
if(v.isPoint()){
v2.beginLoc=v2.endLoc=dest1[2]-1;
}else{
v2.beginLoc=dest2[2];
v2.endLoc=dest1[2];
}
if(v2.call!=null && Tools.isLetter(v2.call.charAt(0)) && !v2.call.equalsIgnoreCase("ref")){
v2.call=AminoAcid.reverseComplementBases(v2.call);
}
if(v2.ref!=null && Tools.isLetter(v2.ref.charAt(0)) && !v2.ref.equalsIgnoreCase("ref")){
v2.ref=AminoAcid.reverseComplementBases(v2.ref);
}
}
assert(v2.endLoc-v2.beginLoc==v.endLoc-v.beginLoc) : "\n\n"+v.toSourceString()+"\n\n"+v2.toSourceString()+
"\n\n"+v.beginLoc+" -> "+Arrays.toString(dest1)+
"\n\n"+v.endLoc+" -> "+Arrays.toString(dest2)+
"\n\n"+cl+"\n\n";
assert(v2.beginLoc<=v2.endLoc) : "\n\n"+v.toSourceString()+"\n\n"+v2.toSourceString()+
"\n\n"+v.beginLoc+" -> "+Arrays.toString(dest1)+
"\n\n"+v.endLoc+" -> "+Arrays.toString(dest2)+
"\n\n"+cl+"\n\n";
v2.intern();
return v2;
}
public Variation translate(Variation v){
if(v.getClass()==VarLine.class){
return translate((VarLine)v);
}
assert(v.getClass()==Variation.class);
ChainLine[] array=lines[v.chromosome];
int index=ChainLine.binarySearch(v.beginLoc, array);
if(index<0){return null;}
ChainLine cl=array[index];
if(!cl.contains(v.beginLoc, v.endLoc)){return null;}
int[] dest1=cl.translate(v.beginLoc);
int[] dest2=cl.translate(v.endLoc);
if(dest1==null || dest2==null){return null;}
Variation v2=v.clone();
if(cl.qStrand==Shared.PLUS){
v2.chromosome=(byte)dest1[0];
v2.beginLoc=dest1[2];
v2.endLoc=dest2[2];
}else{
// assert(false) : "TODO";
v2.chromosome=(byte)dest1[0];
if(v.isPoint()){
v2.beginLoc=v2.endLoc=dest1[2]-1;
}else{
v2.beginLoc=dest2[2];
v2.endLoc=dest1[2];
}
if(v2.call!=null && Tools.isLetter(v2.call.charAt(0)) && !v2.call.equalsIgnoreCase("ref")){
v2.call=AminoAcid.reverseComplementBases(v2.call);
}
if(v2.ref!=null && Tools.isLetter(v2.ref.charAt(0)) && !v2.ref.equalsIgnoreCase("ref")){
v2.ref=AminoAcid.reverseComplementBases(v2.ref);
}
}
assert(v2.endLoc-v2.beginLoc==v.endLoc-v.beginLoc) : "\n\n"+v.toSourceString()+"\n\n"+v2.toSourceString()+
"\n\n"+v.beginLoc+" -> "+Arrays.toString(dest1)+
"\n\n"+v.endLoc+" -> "+Arrays.toString(dest2)+
"\n\n"+cl+"\n\n";
assert(v2.beginLoc<=v2.endLoc) : "\n\n"+v.toSourceString()+"\n\n"+v2.toSourceString()+
"\n\n"+v.beginLoc+" -> "+Arrays.toString(dest1)+
"\n\n"+v.endLoc+" -> "+Arrays.toString(dest2)+
"\n\n"+cl+"\n\n";
v2.intern();
return v2;
}
public final int fromBuild;
public final int toBuild;
public final ChainLine[][] lines;
}
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