/**
* @param other another state to check for the quality with.
* @return true if the other state is or possibly is equal to this state, taking ambiguities into
* account, i.e. if the ambiguity sets of this and the other state intersect.
*/
public boolean possiblyEqual(State other) {
for (State state : getCanonicalStates()) {
for (State state1 : other.getCanonicalStates()) {
if (state.equals(state1)) return true;
}
}
return false;
}
/**
* Determine how much in common these potentially ambigous states have as a fraction between 0 and
* 1 2 non-ambiguous states will return 0. 2 identical non-ambigoues states will 1. e.g. for
* Nucleotides R,A = 0.5 R,G = 0.5 R,M = 0.25
*
* @param other another state to compare with
* @return the fraction of canonical states that the 2 potentially ambiguous states have in common
* between 0 and 1.
*/
public double fractionEqual(State other) {
int totalStates = 0;
int sameStates = 0;
if (isGap() || other.isGap()) {
return 1.0;
}
for (State state : getCanonicalStates()) {
for (State state1 : other.getCanonicalStates()) {
totalStates++;
if (state.equals(state1)) {
sameStates++;
}
}
}
return ((double) sameStates) / totalStates;
}