// Convert a Kmer into a string of bases
func Format(kmer Kmer, k int, alpha alphabet.Alphabet) (string, error) {
if alpha.Len() != 4 {
return "", ErrBadAlphabet
}
kmertext := make([]byte, k)
for i := k - 1; i >= 0; i, kmer = i-1, kmer>>2 {
kmertext[i] = byte(alpha.Letter(int(kmer & 3)))
}
return string(kmertext), nil
}
func makeTable(alpha alphabet.Alphabet, alnmat mat) align.SW {
match := alnmat[0]
mismatch := alnmat[1]
gap := alnmat[2]
sw := make(align.SW, alpha.Len())
for i := range sw {
row := make([]int, alpha.Len())
for j := range row {
row[j] = mismatch
}
row[i] = match
sw[i] = row
}
for i := range sw {
sw[0][i] = gap
sw[i][0] = gap
}
return sw
}
// 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
}
func (a Fitted) alignQLetters(rSeq, qSeq alphabet.QLetters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a)
la := make([]int, 0, let*let)
for _, row := range a {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
index := alpha.LetterIndex()
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([]int, r*c)
for j := range table[1:c] {
table[j+1] = table[j] + la[index[qSeq[j].L]]
}
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1].L]
qVal = index[qSeq[j-1].L]
)
if rVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in rSeq", rSeq[i-1].L, i-1)
}
if qVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in qSeq", qSeq[j-1].L, j-1)
}
p := i*c + j
diagScore := table[p-c-1] + la[rVal*let+qVal]
upScore := table[p-c] + la[rVal*let]
leftScore := table[p-1] + la[qVal]
table[p] = max3(diagScore, upScore, leftScore)
}
}
if debugFitted {
drawFittedTableQLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last := 0, diag
max := minInt
var (
i int
j = c - 1
qVal int
)
for {
qVal = index[qSeq[j-1].L]
if qVal >= 0 {
break
}
j--
}
for y := 1; y < r; y++ {
v := table[(y*c)+c-1]
rVal := index[rSeq[y-1].L]
if rVal < 0 {
continue
}
if v >= max && la[rVal*let+qVal] >= 0 {
i = y
max = v
}
}
maxI, maxJ := i, j
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1].L]
qVal = index[qSeq[j-1].L]
)
switch p := i*c + j; table[p] {
case table[p-c-1] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c-1]
i--
j--
last = diag
case table[p-c] + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c]
i--
last = up
case table[p-1] + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-1]
j--
last = left
default:
panic(fmt.Sprintf("align: fitted nw internal error: no path at row: %d col:%d\n", i, j))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a SWAffine) alignLetters(rSeq, qSeq alphabet.Letters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a.Matrix)
if let < alpha.Len() {
return nil, ErrMatrixWrongSize{Size: let, Len: alpha.Len()}
}
la := make([]int, 0, let*let)
for _, row := range a.Matrix {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([][3]int, r*c)
var (
index = alpha.LetterIndex()
maxS, maxI, maxJ = 0, 0, 0
score int
scores [3]int
)
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
p := i*c + j
scores = [3]int{
diag: table[p-c-1][diag],
up: table[p-c-1][up],
left: table[p-c-1][left],
}
score = max(&scores)
matched := score == scores[diag]
score += la[rVal*let+qVal]
switch {
case score > 0:
if score >= maxS && matched {
maxS, maxI, maxJ = score, i, j
}
default:
score = 0
}
table[p][diag] = score
score = max2(
table[p-c][diag]+a.GapOpen+la[rVal*let],
table[p-c][up]+la[rVal*let],
)
if score < 0 {
score = 0
}
table[p][up] = score
score = max2(
table[p-1][diag]+a.GapOpen+la[qVal],
table[p-1][left]+la[qVal],
)
if score < 0 {
score = 0
}
table[p][left] = score
}
}
if debugSmithAffine {
drawSWAffineTableLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last, layer := 0, diag, diag
i, j := maxI, maxJ
loop:
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
switch p := i*c + j; table[p][layer] {
case 0:
break loop
case table[p-c][up] + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][up]
i--
layer = up
last = up
case table[p-1][left] + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][left]
j--
layer = left
last = left
case table[p-c][diag] + a.GapOpen + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][diag]
i--
layer = diag
last = up
case table[p-1][diag] + a.GapOpen + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][diag]
j--
layer = diag
last = left
case table[p-c-1][diag] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][diag]
i--
j--
layer = diag
last = diag
case table[p-c-1][up] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][up]
i--
j--
layer = up
last = diag
case table[p-c-1][left] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][left]
i--
j--
layer = left
last = diag
default:
panic(fmt.Sprintf("align: sw affine internal error: no path at row: %d col:%d layer:%s\n", i, j, "mul"[layer:layer+1]))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a SW) alignLetters(rSeq, qSeq alphabet.Letters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a)
la := make([]int, 0, let*let)
for _, row := range a {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([]int, r*c)
var (
index = alpha.LetterIndex()
maxS, maxI, maxJ = 0, 0, 0
score int
scores [3]int
)
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
p := i*c + j
scores = [3]int{
diag: table[p-c-1] + la[rVal*let+qVal],
up: table[p-c] + la[rVal*let],
left: table[p-1] + la[qVal],
}
score = max(&scores)
switch {
case score > 0:
if score >= maxS && score == scores[diag] {
maxS, maxI, maxJ = score, i, j
}
default:
score = 0
}
table[p] = score
}
}
if debugSmith {
drawSWTableLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last := 0, diag
i, j := maxI, maxJ
loop:
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
switch p := i*c + j; table[p] {
case 0:
break loop
case table[p-c-1] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c-1]
i--
j--
last = diag
case table[p-c] + la[rVal*let]:
if last != up {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c]
i--
last = up
case table[p-1] + la[qVal]:
if last != left {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-1]
j--
last = left
default:
panic(fmt.Sprintf("align: sw internal error: no path at row: %d col:%d\n", i, j))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a SW) alignQLetters(rSeq, qSeq alphabet.QLetters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a)
if let < alpha.Len() {
return nil, ErrMatrixWrongSize{Size: let, Len: alpha.Len()}
}
la := make([]int, 0, let*let)
for _, row := range a {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([]int, r*c)
var (
index = alpha.LetterIndex()
maxS, maxI, maxJ = 0, 0, 0
score int
)
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1].L]
qVal = index[qSeq[j-1].L]
)
if rVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in rSeq", rSeq[i-1].L, i-1)
}
if qVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in qSeq", qSeq[j-1].L, j-1)
}
p := i*c + j
diagScore := table[p-c-1] + la[rVal*let+qVal]
upScore := table[p-c] + la[rVal*let]
leftScore := table[p-1] + la[qVal]
score = max3(diagScore, upScore, leftScore)
switch {
case score > 0:
if score >= maxS && score == diagScore {
maxS, maxI, maxJ = score, i, j
}
default:
score = 0
}
table[p] = score
}
}
if debugSmith {
drawSWTableQLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last := 0, diag
i, j := maxI, maxJ
loop:
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1].L]
qVal = index[qSeq[j-1].L]
)
switch p := i*c + j; table[p] {
case 0:
break loop
case table[p-c-1] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c-1]
i--
j--
last = diag
case table[p-c] + la[rVal*let]:
if last != up {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c]
i--
last = up
case table[p-1] + la[qVal]:
if last != left {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-1]
j--
last = left
default:
panic(fmt.Sprintf("align: sw internal error: no path at row: %d col:%d\n", i, j))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a NWAffine) alignLetters(rSeq, qSeq alphabet.Letters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a.Matrix)
la := make([]int, 0, let*let)
for _, row := range a.Matrix {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
index := alpha.LetterIndex()
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([][3]int, r*c)
table[0] = [3]int{
diag: 0,
up: minInt,
left: minInt,
}
table[1] = [3]int{
diag: minInt,
up: minInt,
left: a.GapOpen + la[index[qSeq[0]]],
}
for j := range table[2:c] {
table[j+2] = [3]int{
diag: minInt,
up: minInt,
left: table[j+1][left] + la[index[qSeq[j+1]]],
}
}
table[c] = [3]int{
diag: minInt,
up: a.GapOpen + la[index[rSeq[0]]*let],
left: minInt,
}
for i := 2; i < r; i++ {
table[i*c] = [3]int{
diag: minInt,
up: table[(i-1)*c][up] + la[index[rSeq[i-1]]*let],
left: minInt,
}
}
var scores [3]int
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
p := i*c + j
scores = [3]int{
diag: table[p-c-1][diag],
up: table[p-c-1][up],
left: table[p-c-1][left],
}
table[p][diag] = max(&scores) + la[rVal*let+qVal]
table[p][up] = max2(
add(table[p-c][diag], a.GapOpen+la[rVal*let]),
add(table[p-c][up], la[rVal*let]),
)
table[p][left] = max2(
add(table[p-1][diag], a.GapOpen+la[qVal]),
add(table[p-1][left], la[qVal]),
)
}
}
if debugNeedleAffine {
drawNWAffineTableLetters(rSeq, qSeq, index, table, a)
}
var (
aln []feat.Pair
layer int
)
score, last := 0, diag
i, j := r-1, c-1
t := table[i*c+j]
best := t[0]
for i, s := range t[1:] {
if s > best {
best, layer = s, i+1
}
}
maxI, maxJ := i, j
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
switch p := i*c + j; table[p][layer] {
case table[p-c][up] + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][up]
i--
layer = up
last = up
case table[p-1][left] + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][left]
j--
layer = left
last = left
case table[p-c][diag] + a.GapOpen + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][diag]
i--
layer = diag
last = up
case table[p-1][diag] + a.GapOpen + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][diag]
j--
layer = diag
last = left
case table[p-c-1][up] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][up]
i--
j--
layer = up
last = diag
case table[p-c-1][left] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][left]
i--
j--
layer = left
last = diag
case table[p-c-1][diag] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][diag]
i--
j--
layer = diag
last = diag
default:
panic(fmt.Sprintf("align: nw affine internal error: no path at row: %d col:%d layer:%s\n", i, j, "mul"[layer:layer+1]))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
if i != j {
aln = append(aln, &featPair{
a: feature{start: 0, end: i},
b: feature{start: 0, end: j},
score: table[i*c+j][last],
})
}
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a FittedAffine) alignLetters(rSeq, qSeq alphabet.Letters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a.Matrix)
la := make([]int, 0, let*let)
for _, row := range a.Matrix {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
index := alpha.LetterIndex()
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([][3]int, r*c)
table[0] = [3]int{
diag: 0,
up: minInt,
left: minInt,
}
table[1] = [3]int{
diag: minInt,
up: minInt,
}
table[1][left] = a.GapOpen + la[index[qSeq[0]]]
for j := range table[2:c] {
table[j+2] = [3]int{
diag: minInt,
up: minInt,
left: table[j+1][left] + la[index[qSeq[j+1]]],
}
}
table[c] = [3]int{
diag: minInt,
left: minInt,
}
for i := 2; i < r; i++ {
table[i*c] = [3]int{
diag: minInt,
left: minInt,
}
}
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in rSeq", rSeq[i-1], i-1)
}
if qVal < 0 {
return nil, fmt.Errorf("align: illegal letter %q at position %d in qSeq", qSeq[j-1], j-1)
}
p := i*c + j
diagScore := table[p-c-1][diag]
upScore := table[p-c-1][up]
leftScore := table[p-c-1][left]
table[p][diag] = max3(diagScore, upScore, leftScore) + la[rVal*let+qVal]
table[p][up] = max2(
add(table[p-c][diag], a.GapOpen+la[rVal*let]),
add(table[p-c][up], la[rVal*let]),
)
table[p][left] = max2(
add(table[p-1][diag], a.GapOpen+la[qVal]),
add(table[p-1][left], la[qVal]),
)
}
}
if debugFittedAffine {
drawFittedAffineTableLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last, layer := 0, diag, diag
var (
i int
j = c - 1
)
max := minInt
for y := 1; y < r; y++ {
v := table[(y*c)+c-1][diag]
if v >= max {
i = y
max = v
}
}
maxI, maxJ := i, j
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
switch p := i*c + j; table[p][layer] {
case table[p-c][up] + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][up]
i--
layer = up
last = up
case table[p-1][left] + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][left]
j--
layer = left
last = left
case table[p-c][diag] + a.GapOpen + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c][diag]
i--
layer = diag
last = up
case table[p-1][diag] + a.GapOpen + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-1][diag]
j--
layer = diag
last = left
case table[p-c-1][up] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][up]
i--
j--
layer = up
last = diag
case table[p-c-1][left] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][left]
i--
j--
layer = left
last = diag
case table[p-c-1][diag] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p][layer] - table[p-c-1][diag]
i--
j--
layer = diag
last = diag
default:
panic(fmt.Sprintf("align: fitted nw affine internal error: no path at row: %d col:%d layer:%s\n", i, j, "mul"[layer:layer+1]))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func (a NW) alignLetters(rSeq, qSeq alphabet.Letters, alpha alphabet.Alphabet) ([]feat.Pair, error) {
let := len(a)
if let < alpha.Len() {
return nil, ErrMatrixWrongSize{Size: let, Len: alpha.Len()}
}
la := make([]int, 0, let*let)
for _, row := range a {
if len(row) != let {
return nil, ErrMatrixNotSquare
}
la = append(la, row...)
}
index := alpha.LetterIndex()
r, c := rSeq.Len()+1, qSeq.Len()+1
table := make([]int, r*c)
for j := range table[1:c] {
table[j+1] = table[j] + la[index[qSeq[j]]]
}
for i := 1; i < r; i++ {
table[i*c] = table[(i-1)*c] + la[index[rSeq[i-1]]*let]
}
var scores [3]int
for i := 1; i < r; i++ {
for j := 1; j < c; j++ {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
p := i*c + j
scores = [3]int{
diag: table[p-c-1] + la[rVal*let+qVal],
up: table[p-c] + la[rVal*let],
left: table[p-1] + la[qVal],
}
table[p] = max(&scores)
}
}
if debugNeedle {
drawNWTableLetters(rSeq, qSeq, index, table, a)
}
var aln []feat.Pair
score, last := 0, diag
i, j := r-1, c-1
maxI, maxJ := i, j
for i > 0 && j > 0 {
var (
rVal = index[rSeq[i-1]]
qVal = index[qSeq[j-1]]
)
if rVal < 0 || qVal < 0 {
continue
}
switch p := i*c + j; table[p] {
case table[p-c-1] + la[rVal*let+qVal]:
if last != diag {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c-1]
i--
j--
last = diag
case table[p-c] + la[rVal*let]:
if last != up && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-c]
i--
last = up
case table[p-1] + la[qVal]:
if last != left && p != len(table)-1 {
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
maxI, maxJ = i, j
score = 0
}
score += table[p] - table[p-1]
j--
last = left
default:
panic(fmt.Sprintf("align: nw internal error: no path at row: %d col:%d\n", i, j))
}
}
aln = append(aln, &featPair{
a: feature{start: i, end: maxI},
b: feature{start: j, end: maxJ},
score: score,
})
if i != j {
aln = append(aln, &featPair{
a: feature{start: 0, end: i},
b: feature{start: 0, end: j},
score: table[i*c+j],
})
}
for i, j := 0, len(aln)-1; i < j; i, j = i+1, j-1 {
aln[i], aln[j] = aln[j], aln[i]
}
return aln, nil
}
func genCode(w io.Writer, m string, a alphabet.Alphabet) error {
f, err := os.Open(m)
if err != nil {
return err
}
b, err := ioutil.ReadAll(f)
if err != nil {
return err
}
s := string(b)
var (
ind = a.LetterIndex()
ref []string
perm []int
mat [][]int
row int
lastBlank bool
)
for _, l := range strings.Split(s, "\n") {
nsl := noSpace(l)
switch {
case len(l) == 0:
if !lastBlank {
lastBlank = true
fmt.Fprintln(w, "\t//")
}
case l[0] == ' ':
ref = strings.Fields(nsl)
perm = make([]int, a.Len())
for i, l := range ref {
li := ind[l[0]]
if li < 0 {
continue
}
perm[li] = i
}
mat = make([][]int, a.Len())
for j := range mat {
mat[j] = make([]int, a.Len())
}
fallthrough
case l[0] == '#':
lastBlank = false
fmt.Fprintf(w, "\t// %s\n", l)
default:
lastBlank = false
fmt.Fprintf(w, "\t// %s\n", l)
for col, f := range strings.Fields(nsl)[1:] {
mat[ind[ref[row][0]]][ind[ref[col][0]]], err = strconv.Atoi(f)
if err != nil {
return err
}
}
row++
}
}
fmt.Fprintf(w, "\t%s = [][]int{\n\t\t/* ", strings.Replace(m, ".", "_", -1))
for j := range mat {
fmt.Printf("%c ", toUpper(a.Letter(j)))
}
fmt.Fprintln(w, "*/")
for i := range mat {
fmt.Printf("\t\t/* %c */ {", toUpper(a.Letter(i)))
for j, e := range mat[i] {
fmt.Fprint(w, e)
if j < len(mat[i])-1 {
fmt.Print(", ")
}
}
fmt.Fprintln(w, "},")
}
fmt.Fprintln(w, "\t}")
return nil
}