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package icecream;
public class PolymerTrimmer {
public static boolean parse(String arg, String a, String b){
if(a.equalsIgnoreCase("minPolymer")){
minPolymer=Integer.parseInt(b);
}else if(a.equalsIgnoreCase("minFraction")){
float f=Float.parseFloat(b);
setMinFraction(f);
}else if(a.equalsIgnoreCase("polyerror")){
float f=Float.parseFloat(b);
setMinFraction(1-f);
}else{
return false;
}
return true;
}
public static int testLeft(byte[] bases, char symbol){return testLeft(bases, (byte)symbol);}
public static int testLeft(byte[] bases, byte symbol){
float score=0;
float max=0;
int maxPos=-1;
for(int i=0; i<bases.length && score>=minScore; i++){
byte b=bases[i];
if(b==symbol){
score++;
if(score>max){
max=score;
maxPos=i;
}
}else{
score-=penalty;
}
}
int trim=maxPos+1;
return (trim<minPolymer ? 0 : trim);
}
public static int testRight(byte[] bases, char symbol){return testRight(bases, (byte)symbol);}
public static int testRight(byte[] bases, byte symbol){
float score=0;
float max=0;
int maxPos=bases.length;
for(int i=bases.length-1; i>=0 && score>=minScore; i--){
byte b=bases[i];
if(b==symbol){
score++;
if(score>max){
max=score;
maxPos=i;
}
}else{
score-=penalty;
}
}
int trim=bases.length-maxPos;
return (trim<minPolymer ? 0 : trim);
}
public static void setMinFraction(float f){
assert(f>=0 && f<=1) : f;
minFraction=f;
penalty=(f>=1 ? 99 : ((1f/(1-minFraction))-1));
minScore=(f>=1 ? 0 : -4*penalty);
}
static int minPolymer=5;
private static float minFraction=0.8f;
private static float penalty=(1f/(1-minFraction))-1;
private static float minScore=-4*penalty;
}
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