Interface (Schnittstelle)
We need/provide the following parameters:
Edge length
String/Sequence (lowest level annotation)
Substitution probabilities Preferred:
HashMap<Character,
MagicTable> =⇒ Either complete
HashMap, or probability array for each character separately
Deletion probabilities for each position (prob array) of the given sequence
Probabilities for insertions:
for each position of the given sequence
for each inserted character of the alphabet
Maximal (and minimal?) legth of an insertion/deletion (if needed, treat separately)
An Example could be:
evolve(
double/int edgeLength,
Sequence s,
HashMap<Character,MagicTable> substitutionTable,
Double[] insProb,
Double[] insPos,
Double[] delPos,
int maxLength
){...}
evolve(10, "AGCTAA", ..., new Double[]{0.2,0.2,0.3,0.3}, new Double[]{0.3,0.2,0.2,0.3}, ..., ..., 2);