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package tracker;
import repeat.Palindrome;
import shared.Tools;
import structures.ByteBuilder;
import structures.LongList;
/**
* Tracks palindrome stats to determine which kind occur in a given feature.
*
* @author Brian Bushnell
* @date Sept 3, 2023
*
*/
public class PalindromeTracker {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public void add(final Palindrome p, final int a0, final int b0) {
int tail1=p.a-a0, tail2=b0-p.a;
if(tail1>tail2) {
int x=tail1;
tail1=tail2;
tail2=x;
}
int tailDif=tail2-tail1;
int rlen=b0-a0+1;
plenList.increment(p.plen());
loopList.increment(p.loop());
tailList.increment(tail1);
tailList.increment(tail2);
tailDifList.increment(tailDif);
matchList.increment(p.matches);
mismatchList.increment(p.mismatches);
rlenList.increment(rlen);
found++;
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
public PalindromeTracker add(PalindromeTracker p) {
for(int i=0; i<lists.length; i++) {
lists[i].incrementBy(p.lists[i]);
}
found+=p.found;
return this;
}
public ByteBuilder appendTo(ByteBuilder bb) {
return append(bb, "#Value\tplen\tloop\ttail\ttaildif\tmatch\tmismtch\trlen", lists, histmax);
}
@Override
public String toString() {
return appendTo(new ByteBuilder()).toString();
}
/*--------------------------------------------------------------*/
/*---------------- Static Methods ----------------*/
/*--------------------------------------------------------------*/
/** Can be used to make generic histograms */
public static ByteBuilder append(ByteBuilder bb, String header, LongList[] lists, int histmax) {
int maxSize=1;
for(LongList ll : lists) {
ll.capHist(histmax);
maxSize=Tools.max(maxSize, ll.size);
}
bb.append(header).nl();
for(int i=0; i<maxSize; i++) {
bb.append(i);
for(LongList ll : lists) {
bb.tab().append(ll.get(i));
}
bb.nl();
}
return bb;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
public long found=0;
public LongList plenList=new LongList();
public LongList loopList=new LongList();
public LongList tailList=new LongList();
public LongList tailDifList=new LongList();
public LongList matchList=new LongList();
public LongList mismatchList=new LongList();
public LongList rlenList=new LongList();//Region of interest length
public final LongList[] lists={plenList, loopList, tailList,
tailDifList, matchList, mismatchList, rlenList};
/*--------------------------------------------------------------*/
/*---------------- Statics ----------------*/
/*--------------------------------------------------------------*/
public static int histmax=50;
}
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