// Match generates a penalty matrix for a.
// Perfect matches have penalty match.
// Gaps have penalty gap.
// Everything else has penalty mismatch.
// For example, Match(alphabet.DNA, 0, 1, -1) generates the original Needleman-Wunsch penalty matrix.
func Match(a alphabet.Alphabet, gap, match, mismatch int) [][]int {
l := a.Len()
arr := make([]int, l*l)
g := a.IndexOf(a.Gap())
for i := 0; i < l; i++ {
for j := 0; j < l; j++ {
score := mismatch
switch {
case i == g, j == g:
score = gap
case i == j:
score = match
}
arr[i*l+j] = score
}
}
x := make([][]int, l)
for i := 0; i < l; i++ {
x[i] = arr[i*l : (i+1)*l]
}
return x
}
