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package structures;
import java.util.ArrayList;
import java.util.Collections;
import shared.Tools;
/** A numeric range, assuming 0-based, base-centered numbering,
* including a contig number. */
public class CRange implements Comparable<CRange>{
/*--------------------------------------------------------------*/
public CRange(long c_, int a_, int b_){
this(c_, a_, b_, null);
}
public CRange(long c_, int a_, int b_, Object o_){
a=a_;
b=b_;
c=c_;
obj=o_;
assert(a<=b) : a+">"+b;
}
/*--------------------------------------------------------------*/
public boolean includes(int p){
return p>=a && p<=b;
}
public boolean intersects(int p1, int p2){
return overlap(a, b, p1, p2);
}
public boolean adjacent(int p1, int p2) {
return adjacent(a, b, p1, p2);
}
public boolean touches(int p1, int p2) {
return touch(a, b, p1, p2);
}
public boolean includes(int p1, int p2){
return include(a, b, p1, p2);
}
/*--------------------------------------------------------------*/
public boolean intersects(CRange r){
return c==r.c && intersects(r.a, r.b);
}
public boolean touches(CRange r){
return c==r.c && (intersects(r.a, r.b) || adjacent(r.a, r.b));
}
public boolean includes(CRange r){
return c==r.c && includes(r.a, r.b);
}
public int length() {
return b-a+1;
}
/*--------------------------------------------------------------*/
public CRange merge(CRange r){
assert(touches(r));
CRange r2=new CRange(c, min(a, r.a), max(b, r.b), obj);
assert(r2.includes(this));
assert(r2.includes(r));
assert(r2.length()<=length()+r.length());
return r2;
}
public void absorb(CRange r){
assert(touches(r));
a=min(a, r.a);
b=max(b, r.b);
}
@Override
public int hashCode(){
return Integer.rotateLeft(~a, 16)^b^Long.hashCode(Long.rotateRight(c, 8));
}
@Override
public boolean equals(Object r){
return equals((CRange)r);
}
public boolean equals(CRange r){
return c==r.c &&a==r.a && b==r.b;
}
@Override
public int compareTo(CRange r) {
if(c!=r.c) {return c>r.c ? 1 : -1;}
if(a!=r.a) {return a-r.a;}
return b-r.b;
}
@Override
public String toString(){
return "(c"+c+":"+a+(a==b ? "" : (" - "+b))+")";
}
/*--------------------------------------------------------------*/
public static int mergeList(ArrayList<CRange> ranges, boolean sort) {
if(ranges.size()<2){return 0;}
if(sort){Collections.sort(ranges);}
CRange current=ranges.get(0);
int removed=0;
for(int i=1; i<ranges.size(); i++) {
CRange r=ranges.get(i);
if(current.touches(r)) {
current.absorb(r);
ranges.set(i, null);
removed++;
}else{
current=r;
}
}
if(removed>0){
Tools.condenseStrict(ranges);
}
return removed;
}
public static boolean include(int a1, int b1, int a2, int b2){
assert(a1<=b1 && a2<=b2) : a1+", "+b1+", "+a2+", "+b2;
return a2>=a1 && b2<=b1;
}
public static boolean overlap(int a1, int b1, int a2, int b2){
assert(a1<=b1 && a2<=b2) : a1+", "+b1+", "+a2+", "+b2;
return a2<=b1 && b2>=a1;
}
public static boolean touch(int a1, int b1, int a2, int b2){
assert(a1<=b1 && a2<=b2) : a1+", "+b1+", "+a2+", "+b2;
return a2<=b1+1 && b2>=a1-1;
}
public static boolean adjacent(int a1, int b1, int a2, int b2){
assert(a1<=b1 && a2<=b2) : a1+", "+b1+", "+a2+", "+b2;
return a2==b1+1 && b2==a1-1;
}
private static final int min(int x, int y){return x<y ? x : y;}
private static final int max(int x, int y){return x>y ? x : y;}
/*--------------------------------------------------------------*/
/** Left point, inclusive */
public int a;
/** Right point, inclusive */
public int b;
/** Contig or sequence number */
public final long c;
public Object obj; //For attaching things
}
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