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package align2;
import dna.ChromosomeArray;
import dna.Data;
import structures.IntList;
public class CompressString {
public static void main(String[] args){
String s;
s=compressRepeats(args[0].getBytes(), 1);
s=compress(args[0]);
s=compressRepeatsUltra(args[0].getBytes(), 1, 3, null);
System.out.println(args[0]+"\n"+s);
System.exit(0);
ChromosomeArray cha=Data.getChromosome(1);
byte[] bytes=cha.array;
int letters=0;
for(int i=0; i<bytes.length; i++){if(bytes[i]!='N'){letters++;}}
System.out.println("cha bytes length = "+bytes.length);
System.out.println("cha letters length = "+letters);
System.out.println("min="+cha.minIndex+", max="+cha.maxIndex+", length="+(cha.maxIndex-cha.minIndex+1));
s=compressRepeatsUltra(bytes, 1, 1, null);
System.out.println("compress(1) length: "+s.length());
s=compressRepeatsUltra(bytes, 2, 2, null);
System.out.println("compress(2) length: "+s.length());
s=compressRepeatsUltra(bytes, 3, 3, null);
System.out.println("compress(3) length: "+s.length());
s=compressRepeatsUltra(bytes, 1, 2, null);
System.out.println("compress(1,2) length: "+s.length());
s=compressRepeatsUltra(bytes, 1, 3, null);
System.out.println("compress(1,3) length: "+s.length());
// s=compressRepeatsMultiperiod(bytes, 1, 1, null);
// System.out.println("compress(1) length: "+s.length());
//
// s=compressRepeatsMultiperiod(bytes, 2, 2, null);
// System.out.println("compress(2) length: "+s.length());
//
// s=compressRepeatsMultiperiod(bytes, 3, 3, null);
// System.out.println("compress(3) length: "+s.length());
//
// s=compressRepeatsMultiperiod(bytes, 1, 2, null);
// System.out.println("compress(1,2) length: "+s.length());
//
// s=compressRepeatsMultiperiod(bytes, 1, 3, null);
// System.out.println("compress(1,3) length: "+s.length());
}
public static String compress(String s){
String s1=compressRepeats(s.getBytes(), 1);
String s2=compressRepeats(s1.getBytes(), 2);
String s3=compressRepeats(s2.getBytes(), 3);
return s3;
}
public static String compressRepeats(byte[] array, int period){
StringBuilder sb=new StringBuilder(array.length);
for(int base=0; base<array.length; base++){
//Test for repeats of current pattern (array[i] to array[period-1])
int repeats=countRepeats(array, base, period);
int occurances=repeats+1;
// System.out.println("base = "+base+"\t, repeats = "+repeats);
if(repeats==0){
//Advance pointer by 1
sb.append((char)array[base]);
}else if(repeats==1){
//Still advance pointer by 1
sb.append((char)array[base]);
}else if(repeats==2){
//Jump ahead
base+=period-1;
}else{
//Compress and advance pointer by a factor of period
int log=(32-Integer.numberOfLeadingZeros(repeats+1))-1; //+1 is optional; gives lower compression
// System.out.println("repeats="+repeats+
// ", Integer.highestOneBit("+repeats+")="+Integer.highestOneBit(repeats)+
// ", log="+log+", "+Integer.toBinaryString(repeats));
assert(log>0 && log<=31);
//Append
for(int i=1; i<log; i++){
for(int j=0; j<period; j++){
sb.append((char)array[base+j]);
}
}
base=base+(period*(repeats))-1;
}
}
return sb.toString();
}
public static String compressRepeatsMultiperiod(byte[] array, int minPeriod, int maxPeriod, IntList list){
StringBuilder sb=new StringBuilder(array.length);
for(int base=0; base<array.length; base++){
//Test for repeats of current pattern (array[i] to array[period-1])
int period=0;
int repeats=0;
// for(int x=maxPeriod; x>=minPeriod; x--){
// int temp=countRepeats(array, base, x);
// if(temp>1){
// repeats=temp;
// period=x;
// break;
// }
// }
for(int x=minPeriod; x<=maxPeriod; x++){
int temp=countRepeats(array, base, x);
if(temp>1){
repeats=temp;
period=x;
break;
}
}
int occurances=repeats+1;
// System.out.println("base = "+base+"\t, repeats = "+repeats+"\t, period = "+period);
if(repeats==0){
//Advance pointer by 1
sb.append((char)array[base]);
if(list!=null){list.add(base);}
}else if(repeats==1){
//Still advance pointer by 1
sb.append((char)array[base]);
if(list!=null){list.add(base);}
}
// else if(repeats==2){
// for(int j=0; j<period; j++){
// sb.append((char)array[base+j]);
// }
// //Jump ahead
// base+=2*period-1;
// }
else{
//Compress and advance pointer by a factor of period
int log=(32-Integer.numberOfLeadingZeros(repeats+1))-1; //+1 is optional; gives lower compression
// System.out.println("repeats="+repeats+
// ", Integer.highestOneBit("+repeats+")="+Integer.highestOneBit(repeats)+
// ", log="+log+", "+Integer.toBinaryString(repeats));
assert(log>0 && log<=31);
//Append
for(int i=0; i<log; i++){
for(int j=0; j<period; j++){
sb.append((char)array[base+j]);
if(list!=null){list.add(base+j);}
}
}
base=base+(period*(repeats))-1;
}
}
return sb.toString();
}
public static String compressRepeatsUltra(byte[] array, int minPeriod, int maxPeriod, IntList list){
StringBuilder sb=new StringBuilder(array.length);
for(int base=0; base<array.length; base++){
//Test for repeats of current pattern (array[i] to array[period-1])
int period=0;
int repeats=0;
for(int x=minPeriod; x<=maxPeriod; x++){
int temp=countRepeats(array, base, x);
// System.out.println("*** temp="+temp+" for "+base+", "+x);
if(temp>1){
repeats=temp;
period=x;
break;
}
}
// System.err.println(repeats);
if(repeats==0){
//Advance pointer by 1
sb.append((char)array[base]);
if(list!=null){list.add(base);}
}else if(repeats==1){
//Still advance pointer by 1
sb.append((char)array[base]);
if(list!=null){list.add(base);}
// System.err.println(base);
base=base+(period*(repeats))-1;
// System.err.println(base);
}
// else if(repeats==2){
// for(int j=0; j<period; j++){
// sb.append((char)array[base+j]);
// }
// //Jump ahead
// base+=2*period-1;
// }
else{
//Compress and advance pointer
//Append
for(int j=0; j<period; j++){
sb.append((char)array[base+j]);
if(list!=null){list.add(base+j);}
}
base=base+(period*(repeats))-1;
}
}
return sb.toString();
}
public static int countRepeats(byte[] array, int base, int period){
int max=array.length-period+1;
int matches=0;
boolean fail=false;
for(int loc=base+period; loc<max && !fail; loc+=period){
for(int i=0; i<period && !fail; i++){
if(array[base+i]==array[loc+i]){
matches++;
// System.out.println("base = "+base+", loc = "+loc+", period = "+period+", and "+(base+i)+" == "+(loc+i));
}else{
// System.err.println("failed");
fail=true;
}
}
}
// System.err.println("matches = "+matches);
int repeats=matches/period;
// System.err.println("repeats = "+repeats);
return repeats;
}
}
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