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package barcode;
import dna.AminoAcid;
import structures.ByteBuilder;
public class Transition implements Comparable<Transition> {
public Transition(int pos_, byte ref_, byte query_, long count_) {
pos=pos_;
ref=ref_;
query=query_;
count=count_;
}
public int encode() {return encode(pos, ref, query);}
public static int encode(int pos, int ref, int query) {
int x1=baseToNumber[ref];
assert(x1>=0 && x1<4);//Only defined symbols allowed for ref
int x2=baseToNumber[query];
int idx=((pos<<2)|x1)*5+x2;
return idx;
}
public static Transition decode(int idx) {
int x2=idx%5;
idx/=5;
int x1=idx&3;
idx=idx>>2;
int pos=idx;
byte r=numberToBase[x1];
byte q=numberToBase[x2];
return new Transition(pos, r, q, 0);
}
public ByteBuilder appendTo(ByteBuilder bb) {
return bb.append(pos).tab().append(ref).tab().append(query).tab().append(count);
}
@Override
public int compareTo(Transition b) {
if(count!=b.count) {return count<b.count ? 1 : -1;}
if(pos!=b.pos) {return pos-b.pos;}
if(ref!=b.ref) {return baseToNumber[ref]-baseToNumber[b.ref];}
return baseToNumber[query]-baseToNumber[b.query];
}
public final int pos;
public final byte ref;
public final byte query;
public long count;
private static final byte[] numberToBase=AminoAcid.numberToBase;
private static final byte[] baseToNumber=AminoAcid.baseToNumber4;
}
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