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package repeat;
import shared.Tools;
import structures.ByteBuilder;
public class Palindrome implements Comparable<Palindrome>, Cloneable {
public Palindrome(){}
public Palindrome(int a_, int b_, int matches_, int mismatches_){
set(a_, b_, matches_, mismatches_);
}
public void set(int a_, int b_, int matches_, int mismatches_){
a=a_;
b=b_;
matches=matches_;
mismatches=mismatches_;
}
public void setFrom(Palindrome p){
assert(p!=this);
set(p.a, p.b, p.matches, p.mismatches);
}
public String toString() {
return "("+a+"-"+b+",matches="+matches+",mismatches="+mismatches+")";
}
public String toString(final int a0, final int b0) {
int tail1=a-a0, tail2=b0-b;
return "("+a+"-"+b+",matches="+matches+",mismatches="+mismatches+
",loop="+loop()+",tail1="+Tools.min(tail1,tail2)+
",tail2="+Tools.max(tail1,tail2)+",taildif="+Tools.absdif(tail1,tail2)+")";
}
// public ByteBuilder appendTo(ByteBuilder bb, final int a0, final int b0) {
// int tail1=a-a0, tail2=b0-b;
// int tmin=Tools.min(tail1, tail2), tmax=Tools.max(tail1, tail2);
// int tdif=tail2-tail1;
// bb.append('(').append(a).dash().append(b).comma();
// bb.append('m','=').append(matches).comma();
// bb.append('m','m','=').append(mismatches).comma();
// bb.append('l','=').append(loop()).comma();
// bb.append('t','1','=').append(tmin).comma();
// bb.append('t','2','=').append(tmax).comma();
// bb.append('t','d','=').append(tdif);
// return bb.append(')');
// }
public ByteBuilder appendTo(ByteBuilder bb, final int a0, final int b0) {
int tail1=a-a0, tail2=b0-b;
int tmin=Tools.min(tail1, tail2), tmax=Tools.max(tail1, tail2);
// int tdif=tail2-tail1;
bb.append('(').append(a).dash().append(b).comma();
bb.append('P','=').append(matches+mismatches).comma();
bb.append('M','=').append(matches).comma();
bb.append('L','=').append(loop()).comma();
bb.append('T','=').append(tmin).plus().append(tmax);
return bb.append(')');
}
public int plen() {return matches+mismatches;}
public int length() {return b-a+1;}
public int loop() {return length()-2*matches;}
public Palindrome clear() {
a=b=matches=mismatches=0;
return this;
}
public Palindrome clone() {
Palindrome p=null;
try {p=(Palindrome) super.clone();}
catch (CloneNotSupportedException e) {e.printStackTrace();}
return p;
}
/**
* The greater of the two will have more matches, or fewer mismatches,
* or be longer, or more to the left.
*/
public int compareTo(Palindrome p) {
if(p==null) {return 1;}
if(matches!=p.matches) {return matches-p.matches;}
if(mismatches!=p.mismatches) {return p.mismatches-mismatches;}
int lenDif=length()-p.length();
if(lenDif!=0) {return lenDif;}
return p.a-a;
}
/** Start location */
public int a=0;
/** Stop location */
public int b=0;
/** Length of the palindromic sequence, excluding the loop */
public int matches=0;
/** Number of mismatches in the palindrome */
public int mismatches=0;
}
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