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package org.statmt.hg4;
import java.util.BitSet;
public class Coverage implements Comparable<Coverage> {
BitSet coverage;
int slen;
public Coverage(int phraseSize) {
coverage = new BitSet(phraseSize);
slen = phraseSize;
}
/**
* @param phraseSize
* @param coverageStart
* @param coverageEnd (exclusive)
*/
public Coverage(int phraseSize, int coverageStart, int coverageEnd) {
coverage = new BitSet(phraseSize);
coverage.set(coverageStart,coverageEnd,true);
slen = phraseSize;
System.out.println("C(" + phraseSize + "," + coverageStart + "," + coverageEnd +")");
}
/**
* Takes 'or' of params, asserts compatibility.
* @param a
* @param b
*/
public Coverage(Coverage a, Coverage b) {
assert(a.isCompatible(b));
slen = a.slen;
assert(a.slen == b.slen);
this.coverage = (BitSet)a.coverage.clone();
this.coverage.or(b.coverage);
}
public int size() {
return slen;
}
@Override
public int hashCode() {
return 37 * slen + this.toString().hashCode();
}
@Override
public boolean equals(Object o) {
Coverage c = (Coverage)o;
return this.slen == c.slen && this.toString().equals(c.toString());
}
public int nextGap(int fromIndex) {
int loc = coverage.nextClearBit(fromIndex);
if (loc >= slen) return -1;
else return loc;
}
public int nextCover(int fromIndex) {
return coverage.nextSetBit(fromIndex);
}
/**
* Checks if coverages don't overlap.
* @param other
* @return
*/
public boolean isCompatible(Coverage other) {
assert(this.slen == other.slen);
return !this.coverage.intersects(other.coverage);
}
public boolean isAllCovered() {
return coverage.cardinality() == slen;
}
public int compareTo(Coverage other) {
return other.coverage.cardinality() - this.coverage.cardinality();
}
public String toString() { return coverage.toString() + " size="+this.size(); }
}
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