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package driver;
import dna.AminoAcid;
import dna.ChromosomeArray;
import dna.Data;
import dna.Gene;
import shared.Shared;
import shared.Tools;
import structures.Range;
public class GetSequence {
public static void main(String[] args){
int chrom=-1;
byte strand=Shared.PLUS;
/** Change base to zero or one for the coordinates mode */
int base=0;
// char c=args[1].charAt(0);
// if(c=='+'){strand=Gene.PLUS;}
// else if(c=='-'){strand=Gene.MINUS;}
// else{assert(false) : "Invalid strand: "+args[1];}
int firstLoc=-1;
for(int i=0; i<args.length && firstLoc<0; i++){
char x=args[i].charAt(0);
if(args[i].startsWith("build")){
final String arg=args[i];
final String[] split=arg.split("=");
Data.setGenome(Integer.parseInt(split[1]));
}else if(Tools.isDigit(x) || x=='[' || x=='('){
firstLoc=i;
}else{
if(args[i].startsWith("chr")){
chrom=Gene.toChromosome(args[i]);
}else if(x=='b'){
// Data.GENOME_BUILD=Gene.toBuild(args[i]);
Data.setGenome(Gene.toBuild(args[i]));
}else if(x=='+' || x=='-'){
strand=Gene.toStrand(args[i]);
}else{
assert(false) : "Bad parameter: "+args[i];
}
}
}
// System.out.println(Data.GENOME_BUILD);
// System.out.println(chrom);
// System.out.println(strand);
assert(strand==Shared.PLUS) : "TODO";
ChromosomeArray cha=Data.getChromosome(chrom);
String[] array=new String[args.length];
// System.out.println("firstLoc="+firstLoc+"/"+args.length);
for(int i=firstLoc; i<args.length; i++){
// System.out.println("Processing "+args[i]);
args[i]=args[i].replace("[","").replace("]","").replace("(","").replace(")","").replace(",","").trim();
Range r=Range.toRange(args[i]);
array[i]=cha.getString((int)r.a-base, (int)r.b-base);
}
String combined="";
System.out.println("Chrom Bounds: "+cha.minIndex+"-"+cha.maxIndex+" ("+cha.array.length+")");
for(int i=firstLoc; i<array.length; i++){
System.out.println("\nchr"+chrom+" ("+args[i]+") = \n"+array[i]);
// System.out.println("AAs:\t"+AminoAcid.stringToAAs(array[i]));
combined+=array[i];
String s=AminoAcid.reverseComplementBases(array[i]);
System.out.println("\n"+s+" (rcomp)");
// System.out.println("AAs:\t"+AminoAcid.stringToAAs(s));
}
System.out.println("\nAAs:\n"+AminoAcid.stringToAAs(combined));
System.out.println("\nAAs (reverse comp):\n"+AminoAcid.stringToAAs(AminoAcid.reverseComplementBases(combined)));
}
public static byte get(int chrom, int a){
ChromosomeArray cha=Data.getChromosome(chrom);
return cha.get(a);
}
public static String get(int chrom, int a, int b){
return get(chrom, a, b, Shared.PLUS);
}
public static String get(int chrom, int a, int b, byte strand){
assert(strand==Shared.PLUS) : "TODO";
ChromosomeArray cha=Data.getChromosome(chrom);
return cha.getString(a, b);
}
}
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