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package dna;
import java.util.Arrays;
public class MotifMulti extends Motif {
public MotifMulti(String name_, Motif...args){
super(name_, args[0].length, args[0].center);
commonLetters=Arrays.toString(args);
sub=args;
}
@Override
public boolean matchesExactly(byte[] source, int a){
for(int i=0; i<sub.length; i++){
Motif m=sub[i];
if(m.matchesExactly(source, a)){
return true;
}
}
return false;
}
@Override
public boolean matchesExtended(byte[] source, int a){
for(int i=0; i<sub.length; i++){
Motif m=sub[i];
if(m.matchesExtended(source, a)){
return true;
}
}
return false;
}
@Override
public float normalize(double strength){
return (float)strength;
// throw new RuntimeException("MotifMulti can't normalize without knowing the submotif.");
}
@Override
public float matchStrength(byte[] source, int a){
float max=0;
for(int i=0; i<sub.length; i++){
Motif m=sub[i];
float temp=m.matchStrength(source, a);
temp=m.normalize(temp);
max=max(max, temp);
}
return max;
}
@Override
public int numBases() {
return sub[0].numBases();
}
public final Motif[] sub;
}
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