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package aligner;
/** FlatAligner with flatter weights */
public final class FlatAligner2 {
public FlatAligner2(){}
/**
* @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
*/
public AlignmentResult alignForward(final byte[] query, final byte[] ref, final int rstart, final int rstop, final int minScore,
final float minRatio) {
// if(ref.length<16300){return ica16.alignForward(query, ref, qstart, rstart, rstop, minScore, minRatio);}
final int arrayLength=rstop-rstart+1;
// if(array1==null || arrayLength+1>array1.length){
// array1=new int[(int)((arrayLength+2)*1.2)];
// array2=new int[(int)((arrayLength+2)*1.2)];
// }
//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;
// currentRstart=minViableRstart;
// System.err.println("qPos="+qpos+", maxScoreThisPass="+maxScoreThisPass+", maxScore="+maxScore+", minScore="+minScore);
// System.err.println(Arrays.toString(prev));
// System.err.println(Arrays.toString(next));
if(maxScoreThisPass<minScore){//Aggressive early exit
// System.err.print('.');
// System.err.println("qPos="+qpos+", maxScoreThisPass="+maxScoreThisPass+", maxScore="+maxScore+", minScore="+minScore);
return null;
}
{//Safe early exit
// if((maxScoreThisPass+remaining+query.length)/2<minPassingScore){return null;}
// if((maxScoreThisPass+remaining+query.length)<minPassingScore2){return null;}
if(maxScoreThisPass<minViableScore){return null;}
}
int[] temp=prev;
prev=next;
next=temp;
}
// System.err.print('*');
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+query.length)/2;//Rescale 0 to length
maxScore=(maxScore-pointsSub*query.length)/(pointsMatch-pointsSub);//Rescale 0 to length
final float ratio=maxScore/(float)query.length;
// System.err.println("maxqPos="+maxQpos+", maxScore="+maxScore+", minScore="+(minRatio*query.length));
// if(minRatio*query.length>maxScore){return null;}
if(ratio<minRatio){return null;}
// System.err.print('^');
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
*/
public AlignmentResult alignForwardShort(final byte[] query, final byte[] ref, final int rstart, final int rstop,
final float minRatio) {
// if(ref.length<16300){return ica16.alignForwardShort(query, ref, qstart, rstart, rstop, minScore, minRatio);}
final int arrayLength=query.length;
// if(array1==null || arrayLength+1>array1.length){
// array1=new int[(int)((arrayLength+2)*1.2)];
// array2=new int[(int)((arrayLength+2)*1.2)];
// }
//Stack allocated; faster.
final int[] array1=new int[arrayLength+1], array2=new int[arrayLength+1];
final int minPassingScore=(int)(pointsMatch*query.length*minRatio);
int[] prev=array1, next=array2;
int maxScore=-1;
int maxQpos=-1;
int maxRpos=-1;
for(int i=0; i<prev.length; i++) {
prev[i]=pointsIns*i;
}
for(int rpos=rstart; rpos<=rstop && maxScore<minPassingScore; rpos++){
if(rstop-rpos<arrayLength){prev[0]=next[0]+pointsDel;}
final byte r=ref[rpos];
int score=0;
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=Tools.max(vScore, hScore, dScore);
score=(dScore>=vScore ? dScore : vScore);
score=(hScore>score ? hScore : score);
next[apos]=score;
}
itersShort+=arrayLength;
if(score>=maxScore){
maxScore=score;
maxQpos=arrayLength-1;
maxRpos=rpos;
}
// System.err.println("qPos="+qpos+", maxScoreThisPass="+maxScoreThisPass+", maxScore="+maxScore+", minScore="+minScore);
// System.err.println(Arrays.toString(prev));
// System.err.println(Arrays.toString(next));
// if(maxScoreThisPass<minScore){//Aggressive early exit
//// System.err.print('.');
//// System.err.println("qPos="+qpos+", maxScoreThisPass="+maxScoreThisPass+", maxScore="+maxScore+", minScore="+minScore);
// return null;
// }
// {//Safe early exit
// int remaining=query.length-qpos;
//// if((maxScoreThisPass+remaining+query.length)/2<minPassingScore){return null;}
//// if((maxScoreThisPass+remaining+query.length)<minPassingScore2){return null;}
// if((maxScoreThisPass+remaining)<minPassingScore3){return null;}
// }
int[] temp=prev;
prev=next;
next=temp;
}
// System.err.print('*');
// 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;
// }
// }
final float ratio=maxScore/(float)(pointsMatch*query.length);
// System.err.println(ratio+"\t"+maxScore+"\t"+query.length);
// System.err.println("maxqPos="+maxQpos+", maxScore="+maxScore+", minScore="+(minRatio*query.length));
// if(minRatio*query.length>maxScore){return null;}
if(ratio<minRatio){return null;}
// System.err.print('^');
return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ratio);
}
/*--------------------------------------------------------------*/
/*---------------- Getters ----------------*/
/*--------------------------------------------------------------*/
long iters(){return iters;}
long itersShort(){return itersShort;}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
long iters = 0;
long itersShort = 0;
/*--------------------------------------------------------------*/
/*---------------- Constants ----------------*/
/*--------------------------------------------------------------*/
public static final int pointsMatch = 10;
public static final int pointsSub = -9;
public static final int pointsDel = -11;
public static final int pointsIns = -11;
}
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