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package var2;
import shared.Tools;
import structures.ByteBuilder;
public class SoftClipper {
public static byte[] softClipMatch(byte[] match, int minClipLength, boolean allowMutation,
final int oldStart, final int oldStop, final int[] startStopRvec){
final int matchScore=100;
final int subScore=-200;
final int subScore2=-100;
final int insScore=-200;
final int delScore=-200;
final int delScore2=-10;
final int clipScore=-1;
final int nScore=1;
int insCount=0;
int delCount=0;
long score=0;
long maxScore=0;
int maxPos=-1;
int maxStart=-1;
int currentStart=-1;
byte current='?';
for(int mpos=0; mpos<match.length; mpos++){
final byte m=match[mpos];
// long prevScore=score;
if(m=='m' || m=='N' || m=='R'){
if(score==0){currentStart=mpos;}
score=score+(m=='m' ? matchScore : nScore);
if(score>maxScore){
maxScore=score;
maxPos=mpos;
maxStart=currentStart;
}
}else{
if(m=='S' || m=='s'){
score=score+(m==current ? subScore2 : subScore);
}else if(m=='D'){
score=score+(m==current ? delScore2 : delScore);
delCount++;
}else if(m=='I' || m=='X' || m=='Y'){
score=score+insScore;
insCount++;
}else if(m=='C'){
score=score+clipScore;
}
score=Tools.max(0, score);
}
current=m;
}
if(maxScore<1){return match;}
final int leftClipM=maxStart;
final int rightClipM=(match.length-maxPos-1);
int leftClip=0, rightClip=0;
for(int i=0; i<match.length; i++){
byte m=match[i];
if(i<maxStart){
leftClip+=(m=='D' ? 0 : 1);
}else if(i>maxPos){
rightClip+=(m=='D' ? 0 : 1);
}
}
if(leftClip<minClipLength && rightClip<minClipLength){return match;}
int start=oldStart, stop=oldStop;
if(delCount==0){
final byte[] array=allowMutation ? match : match.clone();
for(int i=0; i<leftClip; i++){array[i]='C';}
for(int i=0, j=array.length-1; i<rightClip; i++, j--){array[j]='C';}
startStopRvec[0]=start;
startStopRvec[1]=stop;
return array;
}
ByteBuilder bb=new ByteBuilder(match.length);
if(leftClip>=minClipLength){
for(int mpos=0, processed=0; mpos<match.length; mpos++){
byte m=match[mpos];
if(mpos>=leftClipM){
bb.append(m);
}else{
if(m=='D'){
start++;
}else if(m=='I'){
start--;
bb.append('C');
processed++;
}else{
bb.append('C');
processed++;
}
}
}
}else{
bb.append(match);
}
if(rightClip>=minClipLength){
bb.reverseInPlace();
byte[] temp=bb.toBytes();
bb.clear();
for(int mpos=0, processed=0; mpos<temp.length; mpos++){
byte m=temp[mpos];
if(mpos>=rightClipM){
bb.append(m);
}else{
if(m=='D'){
stop--;
}else if(m=='I'){
stop++;
bb.append('C');
processed++;
}else{
bb.append('C');
processed++;
}
}
}
bb.reverseInPlace();
}
startStopRvec[0]=start;
startStopRvec[1]=stop;
return bb.toBytes();
}
}
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