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package structures;
import shared.Tools;
public class SeqPos implements Cloneable, Comparable<SeqPos>{
// public SeqPos(byte[] seq_, int pos_) {this(seq_, pos_, 1);}
public SeqPos(SeqPos sp) {this(sp.seq, sp.pos, sp.count, sp.hashcode, sp.gc, sp.score);}
// public SeqPos(byte[] seq_, int pos_, int count_) {
//// synchronized(this) {
// seq=seq_;
// pos=pos_;
// count=count_;
// hashcode=Tools.hash(seq, 22);
// gc=Tools.calcGC(seq);
// assert(count>=0);
//// }
// }
SeqPos(byte[] seq_, int pos_, int count_, int code_, float gc_, float score_) {
// synchronized(this) {
seq=seq_;
pos=pos_;
count=count_;
hashcode=code_;
gc=gc_;
score=score_;
assert(count>=0);
// }
}
// public void setFrom(SeqPos sp) {
// synchronized(sp) {
// synchronized(sp.seq) {synchronized(this) {
// seq=sp.seq;
// pos=sp.pos;
//// count=sp.count;
// hashcode=sp.hashcode;
// assert(count>0);
// }}
// }
// }
@Override
public boolean equals(Object o) {
return equals((SeqPos)o);
}
public boolean equals(SeqPos o) {
if(pos!=o.pos || hashcode!=o.hashcode) {return false;}
return Tools.equals(seq, o.seq);
}
@Override
public int hashCode() {
return hashcode;
}
@Override
public SeqPos clone() {
try {
return (SeqPos) super.clone();
} catch (CloneNotSupportedException e) {
throw new RuntimeException(e);
}
}
@Override
public int compareTo(SeqPos o) {
if(count!=o.count) {return o.count-count;}
if(seq.length!=o.seq.length) {return o.seq.length-seq.length;}
if(score!=o.score) {return o.score>score ? 1 : -1;}
// if(gc!=o.gc) {
// return Tools.absdif((int)(gc*100), 50)<Tools.absdif((int)(o.gc*100), 50) ? -1 : 1;
// }//Neutral gc first
// return Tools.compare(seq, o.seq);
return 0;
}
public final byte[] seq() {return seq;}
public final int pos() {return pos;}
public final byte[] seq;
public final int pos;
public final int hashcode;
public final int count;
public final float gc;
public final float score;
}
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