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package icecream;
import aligner.AlignmentResult;
public final class IceCreamAlignerJava extends IceCreamAligner {
IceCreamAlignerJava(){}
/**
* @param query
* @param ref
* @param rstart
* @param rstop
* @param minScore Quit early if score drops below this
* @param minRatio Don't return results if max score is less than this fraction of max possible score
* @return
*/
@Override
public AlignmentResult alignForward(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
final float minRatio) {
final int arrayLength=rstop-rstart+1;
//Stack allocated; faster.
final int[] array1=new int[arrayLength+1], array2=new int[arrayLength+1];
final int minPassingScore=(int)(query.length*minRatio*pointsMatch);
final int minPassingScore3=minPassingScore-query.length*pointsMatch;
int[] prev=array1, next=array2;
int maxScore=-999999;
int maxQpos=-1;
int maxRpos=-1;
for(int i=0; i<=arrayLength-query.length; i++){prev[i]=0;}
for(int i=arrayLength-query.length, score=0; i<=arrayLength; i++, score+=pointsDel) {
prev[i]=score;
}
int currentRstart=rstart;
for(int qpos=0; qpos<query.length; qpos++){
prev[0]=pointsIns*qpos;
final byte q=query[qpos];
int maxScoreThisPass=-9999;
final int remainingBases=(query.length-qpos);
final int remainingPoints=remainingBases*pointsMatch;
final int minViableScore=minPassingScore3-remainingPoints;
// int minViableRstart=rstop+1;
for(int rpos=currentRstart, apos=1+currentRstart-rstart; rpos<=rstop; rpos++, apos++){
final byte r=ref[rpos];
final boolean match=(q==r);
final int vScore=prev[apos]+pointsIns;
final int hScore=next[apos-1]+pointsDel;
final int dScore=(match ? pointsMatch : pointsSub)+prev[apos-1];
//Slow branchy code
// final int score=Tools.max(vScore, hScore, dScore);
// next[apos]=score;
// if(score>=maxScoreThisPass){
// maxScoreThisPass=score;
// if(score>=maxScore){
// maxScore=score;
// maxQpos=qpos;
// maxRpos=rpos;
// }
// }
//Should be branchless conditional moves
int score=(dScore>=vScore ? dScore : vScore);
score=(hScore>score ? hScore : score);
next[apos]=score;
maxScoreThisPass=(score>maxScoreThisPass ? score : maxScoreThisPass);
// minViableRstart=((score<minViableScore || rpos>minViableRstart) ? minViableRstart : rpos);
}
iters+=arrayLength;
if(maxScoreThisPass<minScore){//Aggressive early exit
return null;
}
{//Safe early exit
if(maxScoreThisPass<minViableScore){return null;}
}
int[] temp=prev;
prev=next;
next=temp;
}
maxScore=-999999;
for(int rpos=rstart, apos=1; rpos<=rstop; rpos++, apos++){//Grab high score from last iteration
int score=prev[apos];
if(score>=maxScore){
maxScore=score;
maxQpos=query.length;
maxRpos=rpos;
}
}
maxScore=(maxScore-pointsSub*query.length)/(pointsMatch-pointsSub);//Rescale 0 to length
final float ratio=maxScore/(float)query.length;
if(ratio<minRatio){return null;}
return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ratio);
}
/**
* @param query
* @param ref
* @param qstart
* @param rstart
* @param rstop
* @param minScore Quit early if score drops below this
* @param minRatio Don't return results if max score is less than this fraction of max possible score
* @return
*/
@Override
public AlignmentResult alignForwardShort(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
final float minRatio) {
final int arrayLength=query.length;
//Stack allocated; faster.
final int[] array1=new int[arrayLength+1], array2=new int[arrayLength+1];
final int minPassingScore=(int)(query.length*minRatio);
final int minPassingScore3=minPassingScore-query.length;
int[] prev=array1, next=array2;
int maxScore=-999999;
int maxQpos=-1;
int maxRpos=-1;
for(int i=0; i<prev.length; i++) {
prev[i]=pointsIns*i;
}
for(int rpos=rstart; rpos<=rstop; rpos++){
if(rstop-rpos<arrayLength){prev[0]=next[0]+pointsDel;}
final byte r=ref[rpos];
int score=0;
//In Java, the unsplit loop is faster
//-XX:+UseSuperWord seems to have no impact on speed.
//Might be worth packing the query and ref into int arrays and trying again.
for(int qpos=0, apos=1; qpos<arrayLength; qpos++, apos++){
final byte q=query[qpos];
final boolean match=(q==r);
final int vScore=prev[apos]+pointsIns;
final int hScore=next[apos-1]+pointsDel;
final int dScore=(match ? pointsMatch : pointsSub)+prev[apos-1];
score=(dScore>=vScore ? dScore : vScore);
score=(hScore>score ? hScore : score);
next[apos]=score;
}
// //Inner DV loop
// for(int qpos=0, apos=1; qpos<arrayLength; qpos++, apos++){
// final int q=query[qpos];
// final boolean match=(q==r);
// final int vScore=prev[apos]+pointsIns;
// final int dScore=(match ? pointsMatch : pointsSub)+prev[apos-1];
//
// score=(dScore>=vScore ? dScore : vScore);
//
// next[apos]=score;
// }
//
// //Inner I loop
// for(int qpos=0, apos=1; qpos<arrayLength; qpos++, apos++){
// final int hScore=next[apos-1]+pointsDel;
//
// score=next[apos];
// score=(hScore>score ? hScore : score);
//
// next[apos]=score;
// }
itersShort+=arrayLength;
if(score>=maxScore){
maxScore=score;
maxQpos=arrayLength-1;
maxRpos=rpos;
}
int[] temp=prev;
prev=next;
next=temp;
}
maxScore=(maxScore-pointsSub*query.length)/(pointsMatch-pointsSub);//Rescale 0 to length
final float ratio=maxScore/(float)query.length;
if(ratio<minRatio){return null;}
return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ratio);
}
/*--------------------------------------------------------------*/
/*---------------- Getters ----------------*/
/*--------------------------------------------------------------*/
@Override
long iters(){return iters;}
@Override
long itersShort(){return itersShort;}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
long iters = 0;
long itersShort = 0;
/*--------------------------------------------------------------*/
/*---------------- Constants ----------------*/
/*--------------------------------------------------------------*/
public static final int pointsMatch = 1;
public static final int pointsSub = -1;
public static final int pointsDel = -2;
public static final int pointsIns = -2;
}
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